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title: "ChangeLog"linkTitle: "ChangeLog"weight: 4description: "ChangeLog"categories: - hometags:
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CHANGELOG

This is a fairly major update to Olex2. The major changes are outlined below.
Reworked Help System for the GUI
You may have noticed that the help system looks different from what it used to be. It is also much more complete -- although nowhere as complete as we would like it to be. The entire help system is generated from MarkDown files which are available from GITHUB, where these files render into some very readable format. This also means that anyone can contribute to our help system -- please request commit permission from us and we will welcome you as a valued contributor. In the long term, we are also planning to make this help available in different languages -- if you can help with a translation, please also let us know.
NoSpherA2 supersedes HARt
The Hirshfeld Atom Refinement team of Simon Grabowsky, Dylan Jayatilaka, and coworkers worked hard on this exciting new refinement tool. It has been superseded by the more powerful NoSpherA2 (available under the Work tab) for refinement involving nonspherical form factors. Note that NoSpherA2 still includes the HARt tool for those wishing to perform Hirshfeld atom refinement.
EXTI
Sometimes it is necessary to refine the extinction, and sometimes it is not. Olex2 now makes this decision automatically (it refines EXTI if the value is twice its e.s.d.). If you un-tick the box, EXTI will not be refined, and if you re-tick the box, it will be refined. You are in control!
No more _publ_* items in the CIF
After many discussions with publishers, the IUCr and the CCDC, we have decided to remove all items starting with _publ_* from our CIF files. These have been replaced with _audit_* instead, since each structure is a 'stand-alone' piece of work and its authors should be clearly known and acknowledged, regardless of where the structure eventually ends up. More info on _audit_author here.

EXTENSION_MODULES

The Extension Modules either provide functionality or make frequently performed tasks easier to do. We are currently working on a number of these modules and will make them available for testing as they are ready. To test and use them, it is necessary to agree to the following conditions:
  1. We take no responsibility for any modules that are in the testing phase. Please use discretion and check everything carefully!
  2. Please tell us about bugs and suggest improvements by sending an email to support-at-olex2.org.
  3. Testing modules will be initially made available for 30 days. After this period, it is possible to renew the module two more times for 30 days at a time. After this period, contact us at support-at-olex2.org to continue using/testing the modules.
  4. Some of these modules will not be available free of charge after the end of the testing phase.

Email
Enter a valid email address, select the module to be installed from the drop-down menu, and press the Install button. An email containing a link to activate the module will be sent to the email address entered here. Click the link to activate the module. After activation, reopen this tool tab and select the requested module again from the drop-down menu. This will install the module, which will be available after restarting Olex2.
Reference
Enter any text here to maintain a record of the machine on which the module has been installed, e.g., My Work Computer.
Modules


List of Extension Modules:  All extension modules that are available for this version of Olex2 (version number and also alpha, beta or release) are found here. Once a module is selected from the drop-down menu, the Please Choose button will change to Install. Press this button to start the installation.

Note: The list of available modules will only be visible when the computer is online  (connected to the internet)! The list will remain empty when offline!
Offline Installation
If it is impossible to perform an online installation of the extension modules, please contact us directly at enquiries@olexsys.org to obtain a .zip file containing the requested module. Save this file somewhere on the computer's hard disk and then point to this location after pressing the "Install Offline" button.

SETTINGS-TARGET

The main settings for Olex2.

ATOM_SETTINGS

Some attributes of how atoms are displayed in Olex2 can be modified within a specific style.
Atom Radius
This slider changes the radius of the selected atoms (in Ball and Stick, or 'pers' mode). Clicking on Set will make this the default radius. The atom radius can be set manually with the 'arad' and 'azoom' line commands, as described below.

arad:  This parameter affects the radius of the selected atoms (or all atoms, if none are selected) in Ball and Stick ('pers') mode only. Typically, the radius in 'pers' mode is taken from a definition file (and is different for different elements). arad overrides these settings. A typical value for H atoms would be:
$+ html.Snippet(GetVar(default_link),"value=arad 0.2","hint=arad 0.2","onclick=arad 0.2","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Sets the radius of the selected atoms(s) to a value of 0.2.


azoom:  This zooms the displayed atom sizes regardless of whether the atoms are shown in Ball and Stick ('pers') or Ellipsoid ('telp') modes. This value is given in percent, and scales the selected atoms.
$+ html.Snippet(GetVar(default_link),"value=azoom 120","hint=azoom 120","onclick=azoom 120","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Scales the selected atom(s) to 120 percent of normal size.
$+ html.Snippet(GetVar(default_link),"value=azoom 100","hint=azoom 100","onclick=azoom 100","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Scales the selected atom(s) to normal size.
In the 'azoom' command, "100" shows the original atom size; larger/smaller values vary the display accordingly.

Note: This setting can play havoc with the ORTEP "50 percent probability' convention. In order to ensure that all atoms are shown with the standard probability, use:
$+ html.Snippet(GetVar(default_link),"value=telp 50","hint=telp 50","onclick=telp 50","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Sets the ADP display to the 50 percent probability level.
The size of the ellipsoids displayed in the screen can be modified by using a different probability level, e.g., to decrease the size slightly from the default value, use:
$+ html.Snippet(GetVar(default_link),"value=telp 30","hint=telp 30","onclick=telp 30","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Sets the ADP display to the 30 percent probability level.

BOND_SETTINGS


Bond Width
Change the radius of the selected bonds. Clicking on Set will make this the default radius. Please note that this will change the radius of all bonds of the same type.
$+ html.Snippet(GetVar(default_link),"value=individualise","hint=individualise","onclick=individualise","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")To set the radius of a single occurrence of a bond, select the bond and type this command first, then change the radius to the desired value.

Style
Choose an overall style setting for all atoms from the drop-down menu.
Bond Colour
Choose the colour of the bonds here. The default is elements: half the bond will be the colour of one atom and the other half the colour of the other atom. Other options may be chosen from the drop-down menu.

BACKGROUND

A choice of different backgrounds is available for Olex2. Depending on the context, sometimes a dark background works better than a light one, and sometimes a graduated background is best. It is possible to switch quickly between them.
Solid Colour/White
F2 will toggle between the solid coloured background (as defined in the scene settings, accessed by right-clicking in the display area and selecting Draw style, then Scene Properties...) and thee solid white background.
Graduated Background
F4 toggles between the solid background and the graduated background.
$+ html.Snippet(GetVar(default_link),"value=grad","hint=grad","onclick=grad","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Sets the colour of the four corners of the graduated background. Double click in each coloured box to set the color of each corner.


Note: With grad -p=filename.png it is possible to set a background picture. This can be very useful, e.g., to compare two different views of a single structure or to compare two different structures side by side on the screen:
  1. First, create a picture of first view of the structure by typing pict 3.png 3 in the console (use a larger/smaller number for a higher/lower resolution picture; type help pict for more information on the pict command). This will create a file called "3.png" in the current working folder. (To find this folder, type user at the console prompt.)
  2. Next, move/rotate the view of the structure, or open a new structure, then type grad -p=3.png. The first picture (3.png in this example) will be displayed as a static screen background to the currently active structure, which can still be moved or rotated as normal.
  3. To remove the picture from the background and return to the normal gradient background type grad -p.

GUI_WIDTH

The width of the GUI (i.e., the panel containing all the Olex2 tool tabs and commands; see image below) can be adjusted to any desired value.



Click one of the built-in links (Default, Narrow, or Wide), or enter an arbitrary value. The font size of the items on the GUI will adjust automatically.
Value < 1
$+ html.Snippet(GetVar(default_link),"value=panel 0.33","hint=panel 0.33","onclick=panel 0.33","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")If the value entered in the box is less than 1, the GUI width will be set to that fraction of the total width. For example, entering 0.33 will divide the display so that the GUI takes up 1/3 of the width and the structure takes up 2/3.

Value > 100
$+ html.Snippet(GetVar(default_link),"value=panel 520","hint=panel 520","onclick=panel 520","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")If the value entered in the box is greater than 100, the absolute width of the GUI will be set to that value, in pixels.

SWAP_HTML_PANEL

Clicking this button switches the position of the GUI between the right and left sides of the Olex2 window.

GUI_LINKS

Set whether some of the links on the GUI are displayed as buttons or as hyperlinks.

TOOLTIPS

If selected, tooltips will be shown when hovering over items in the GUI.

LEGEND

If this box is ticked, a pictogram of all current atom types appears in the main window. With the left mouse button and the SHIFT key pressed, this legend can be moved to any position.
$+ html.Snippet(GetVar(default_link),"value=legend","hint=legend","onclick=legend","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Switch the legend display on or off.
$+ html.Snippet(GetVar(default_link),"value=legend -r","hint=legend -r","onclick=legend -r","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Resets the legend display. Very useful for making an inadvertently moved or deleted legend reappear at the top left of the structure display area.

INFO_BAR

$+ html.Snippet(GetVar(default_link),"value=showwindow info","hint=showwindow info","onclick=showwindow info","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")If selected, more information on a structure is shown in a narrow bar along the top of the display area.

RESET_ALERTS

All hidden alerts will be reset.

CONSOLE_LINES

In order to avoid too much clutter on the GUI, we have decided to provide the console output behind the molecule. Here the number of lines of output can be set to any convenient value. The commands:
$+ html.Snippet(GetVar(default_link),"value=lines 10","hint=lines 10","onclick=lines 10","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will set the console to only show 10 lines. A different number of lines can be chosen.
$+ html.Snippet(GetVar(default_link),"value=lines -1","hint=lines -1","onclick=lines -1","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show all lines of output in the display area.

AUTO_MORE

Keywords entered here control the output of refinement, e.g., MORE -1 dictates the amount of refinement information to be written to the .lst output file; CONF generates a table of torsion angles; BOND $H produces bond length and bond angle information (including bonds to H atoms); and ACTA writes a CIF file to the current working folder.

SAVE_VIEW

If checked, drawing settings such as styles and backgrounds will be saved with the structure. This is somewhat experimental; if things go wrong, it may be necessary to reload the chosen style for that particular structure.

When this box is not checked, then a structure will be loaded with the same style as the previous structure.

START_OLEX2_IN

On startup, Olex2 will open the tab selected from this drop-down menu. This takes effect the next time Olex2 is restarted.

SOLO_MODE

When opening a new tool, all other open tools will automatically be closed.

MODULES_UPDATE

If updates to extension modules are availabe, a pop-up box will appear whenever Olex2 is started. This can be switched off here.

UNIT_CELL_STYLE

The unit cell can be displayed in different ways. First, to make the cell visible:
$+ html.Snippet(GetVar(default_link),"value=cell","hint=cell","onclick=cell","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Switches the unit cell display on.

Cylinder
The unit cell box will be made out of cylinders (i.e., 3D objects).
Lines
The unit cell box will be composed of simple lines.
Width
This sets the thickness of the cylinders or lines.
Colour
Right-click on either the cylinders or lines, then choose Draw Styles. For the lines, there is only a single object to modify; for the cylinders, the little spheres in the corners as well as the cylinders themselves can be modified independently.

USER_DATABASE

Olex2 supports a database of people and their institutions. Set the location of this sqlite database here (a restart is required). The database can also be managed from here.

ENABLE_NETWORK

If this box is not ticked, Olex2 will not communicate with the internet at all, except for checking for updates on startup.

DEBUG_MODE

This setting is for developers only. The switch is to be left off by ordinary users.

PATH

Semicolon-separated strings entered in this box will be added to the System Path as new values before any existing folders. This means that any crystallographic software in the folders listed here will be found by Olex2 first and therefore will be used.

OPENMP

This tool allows for multiprocessing during refinement with olex2.refine using the OpenMP API.

Note: This feature is still under development and may be unstable.

START-TARGET

Start here! - Sample structures - Open existing file - Links to help documentation

OPEN_A_STRUCTURE

Olex2 can read many different crystallographic file formats. The most common way of starting work on a crystal structure is to open a .ins file. Typically, a .hkl file of the same filename as the would have been created by the data processing software at the same time as the .ins file. These two files are all that need to be in the data folder to get started.
Navigate
Navigate to a file by clicking on the Open link under the Start tool, or by using File > Open from the menu bar at the top of Olex2.
Drag and Drop
Alternatively, drag and drop any recognised file into Olex2. This file will then be opened, and the current directory will be set to the one where the file was dragged from.
Command Line
$+ html.Snippet(GetVar(default_link),"value=reap","hint=reap","onclick=reap","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")The reap command opens a file via the file browser. This command can also be followed by a filename: reap sucrose.ins, for example.

SAMPLE_STRUCTURES

We provide some sample structures to experiment with. These sample structures are copied into the Olex2 user area on start-up. If they are deleted, they will come back in their original state on restart.
Sucrose
This very simple structure of sucrose (from our coffee room...) is an ideal structure to get started with.
THPP
An example of a simple disordered structure.
Co110
A simple homoleptic coordination complex of cobalt.
ZP2
A structure with Z' = 2.
Water
A metal complex with bound water molecules and one molecule of water of hydration.
Malbac
A palladium complex with a molecule of toluene across a symmetry element. This is a good example to practice solvent masking, adding molecules with the FragmentDB tool and also to create such a solvent in the structure model from scratch.
Timmy
A continuous solid: Calcium tartrate.

DOCUMENTATION

Here are three sources of information on how to use Olex2.
Online
Searchable and structured documentation is available from the OlexSys website.
Static PDF
We have also provided a PDF manual, which is shipped with this version of Olex2.
Ilia Guzei's Manual
Besides Ilia Guzei's excellent Olex2 user guide which we have linked in the GUI, there is extensive third-party help available online for Olex2 to be found with an internet search.

TUTORIALS-TARGET

A few interactive self-paced tutorials to get started with Olex2

TUTORIAL_HEADER

This panel contains a number of tutorials to instruct the user about the main features of Olex2.
QUICK DEMO
It is recommended to start with the QUICK DEMO tutorial, which gives a general overview of Olex2.
Basic Commands
This tutorial introduces the user to the most commonly issued commands in Olex2.
Growing
In this tutorial, the user is introduced to the important ways of expanding a structure on the screen from the asymmetric unit to packed 3D assemblies (and how to reverse these expansions).
Measurements
The Measurements tutorial deals with how to make geometric measurements on the structure.
Sorting
This tutorial describes the different ways of sorting atoms in a structure with Olex2.
Packing
Crystal packing commands available in Olex2 for examining intermolecular interactions are described in this tutorial.
Mapping & Masks
A large number of mapping and masking tools are available in Olex2; this tutorial shows the user how to employ these tools to analyse a structure.
3D View Tutorial
In this tutorial, the user is introduced to the various ways available for viewing a structure in 3D, with and without special equipment.
Images
Olex2 is capable of making sophisticated graphics files of crystal structures. This tutorial introduces the user to the various options available for creating images of the structure.
Customising the GUI
This tutorial shows how to modify the appearance of the Olex2 GUI to suit one's needs.

BAD_REFLECTIONS_TARGET

Tools for dealing with reflections that do not fit well.

OMIT_REFLECTIONS

The OMIT button applies an OMIT instruction in the instruction file to all reflections for which ||Error/esd|| is greater than the value specified in the box (default 10).

Clicking the ClearOMITs button will delete ALL OMIT instructions, and all previously omitted reflections will be made available again for refinement, except those that are omitted with a general OMIT instruction, e.g., OMIT -3 52.

BAD_REFLECTIONS_SORTING

If this box is ticked, bad reflections will be sorted in order of decreasing ||Error/esd|| once another cycle of refinement is carried out. If, on the other hand, the box is not ticked, bad reflections will be sorted in order from largest positive Error/esd to largest negative Error/esd in the next refinement cycle.

BAD_REFLECTIONS

This panel contains the reflections determined by the refinement program to have the largest values of ||Error/esd||.
Omit all equivalents of a reflection
Exclude an individual reflection (and all its equivalents) by pressing the OMIT link next to it in the list. This will insert the appropriate OMIT command in the instruction file.

EXCLUDE_HKL

Conditions for specific groups of reflections to be excluded can be set here.
Standard Mode (OR)
When the Exclude: link is clicked, all reflections satisfying the specified conditions on h, k, OR l will be omitted from the next refinement cycle.
AND Mode
When the AND box is ticked, the conditions specified for h, k, AND l must be fulfilled for a reflection to be omitted from the refinement when the Exclude: link is clicked.
Reset
Clicking the Reset link clears all currently set exclusion conditions on h, k, and l.

EDIT_REFLECTIONS

It is also possible to omit a particular reflection (e.g., because it was obscured by the beam stop). To do so, click the Edit Reflections link to open a file listing all the bad reflections. Adding a "-" symbol (minus sign) in front of a particular reflection moves it to the bottom of the hkl file (after the "0 0 0" instruction), which instructs the refinement program to ignore it. Replacing the "-" symbol in front of an omitted reflection in this file with a "+" symbol will again include the reflection in the next refinement cycle.

[COMMENT]:_<_HELP_TEXT_FOR_ELECTRON_DENSITY_PEAK_SLIDER_IS_NOW_TAKEN_FROM_TOOLBOX_WORK.MD._>

ELECTRON_DENSITY_TRANSPARENCY_SLIDER

The relative height of Q peaks in the structure is portrayed by their relative transparency: the strongest Q peak is the least transparent and the weakest Q peak is the most transparent. This makes it easy to identify missing heavy (non-hydrogen) atoms in the structure as the least transparent Q peaks. Move the Transparency slider to the right to make the Q peaks more opaqe and to the left to make them more transparent.

ELECTRON_DENSITY_PEAKS

This bar chart lists all the Q peaks and their heights. The bars are colour-coded red, orange, and green, in order of decreasing peak height. Click on a bar to select the corresponding Q peak on the screen.

RECENTLY_OPENED_FILES

This is a list of files that have been recently opened with Olex2. Click on a link to reopen a file.

REFINEMENT-INDICATORS-HELP

REFINEMENT_INDICATORS

This table summarizes the most important information about the diffraction data and the quality of the refinement. If any of these standard indicators are outside the accepted range, they will be highlighted in red. Although this tool tab is called Refinement Indicators, some of the information displayed here (e.g., the various numbers of reflections) is actually solely related to the diffraction data.
R1 (Fo>4σ(Fo))
R1 (Fo>4σ(Fo)) is the R factor calculated using only the strongest reflections, i.e., those with Fo greater than 4σ(Fo).
R1 (all data)
R1 (all data) is the R factor calculated using all reflections.
wR2
wR2 is a weighted R factor based on all reflections, used to track the progress of refinement.
GooF
Goodness of Fit, a calculated parameter used to optimize the weighting scheme during refinement (a weighting scheme producing a GooF close to unity is desirable).
Highest peak
Gives the height of the largest residual electron density peak.
Deepest hole
Gives the negative height ("depth") of the largest residual electron density hole.
Params
Number of parameters (atomic coordinates, displacement parameters, constraints, etc.) used in refinement.
Refs (total)
Total number of reflections in the diffraction data.
Refs (uni)
Number of unique reflections in the diffraction data.
Refs (Fo>4σ(Fo))
Number of strong reflections in the diffraction data, i.e., those with Fo greater than 4σ(Fo).
F000
Structure factor F(000) for the h = k = l = 0 reflection. Counts the number of electrons in the unit cell.
ρ/g*cm-3
Calculated density in g/cm3.
μ/mm-1
Absorption coefficient calculated from the cell contents, density, and radiation wavelength.
Mean Shift
Average change in parameters (atomic coordinates, displacement parameters, etc.) between refinement cycles. A large value of Mean Shift indicates that the refinement has not yet converged, while a value of zero indicates that the refinement has converged.
Max Shift
Maximum change in parameters (atomic coordinates, displacement parameters, etc.) between refinement cycles. A large value of Max Shift indicates that the refinement has not yet converged, while a value of zero indicates that the refinement has converged.

REFLECTION_FILE

It is possible to specify in Olex2 the particular reflection file against which the model is to be refined.
hkl File
Select the .hkl file to be used for refinement from the drop-down menu.
Write Graphics File?
Tick this box to save the reflection statistics graphs generated from the drop-down menu below. Graphs will be saved as .png files in the current working folder for the structure.

REFLECTION_GRAPH

The graphs in this menu are meant to diagnose problems in structure determination. Some of the graphs depend only on the diffraction data, while others depend on the structure model, so it is not strictly accurate to call this tool tab Reflection Statistics.

Select from the drop-down menu the type of graph desired, then click the go button to display the graph. For these graphs, increasing the number of Bins creates a more fine-grained plot by dividing the reflections into more data bins, and ticking the Output csv box writes a text file in .csv format with the data for the current graph to the working folder. When a graph plots resolution along the x-axis, the measure of resolution may be 2θ, d spacing, square of the reciprocal lattice spacing d*, sin(θ)/λ, or (sin(θ)/λ)2, selected from the drop-down menu. Ticking the Write graphics file? box above will save a .png file of the graph in the working folder.
Wilson Plot
This plot provides a statistical comparison of the observed intensity data with the theoretical distribution expected for a random atomic arrangement, taking into account that atomic scattering decreases with increasing 2θ. It is usually linear. The overall displacement parameter B for the structure and scale factor K for the data are derived from this plot. The <||E2 - 1||> statistic shown below the plot helps distinguish between centrosymmetric (centric) and non-centrosymmetric (acentric) structures. If <||E2 - 1||> ≈ 0.968, the structure is likely to be centrosymmetric, but if it is closer to 0.736, the structure is likely non-centrosymmetric. Choose either the built-in Olex2 method or the cctbx method.
Cumulative Intensity
This graph assists in determining whether the structure is centrosymmetric or non-centrosymmetric. If the plotted data lie mostly along the top black line, the structure is likely to be centrosymmetric; if along the middle blue line, the structure is likely non-centrosymmetric. Finally, if the data lie along the bottom red line, it is likely that the structure is non-centrosymmetric and twinned.
Systematic Absences
This plots the intensity distribution for any reflections that are expected to be systematically absent. The intensities of these reflections should be very low and insignificant relative to the standard error of each reflection.
Fobs-Fcalc
This plot of Fobs vs Fcalc is normally a straight line with Fobs about equal to Fcalc throughout their range, i.e., the slope of the line should be about 1 and the intercept about 0. Any omitted reflections are shown in grey. Hovering over a yellow reflection with a mouse shows a readout in the format "OMIT h k l". If the reflection is clicked, an OMIT instruction is added to the instruction file for that reflection, and it turns grey. This is useful for removing an outlying reflection from the refinement, e.g., if the reflection is obscured by the beamstop. Clicking on a grey reflection removes its OMIT instruction and reintroduces it into the refinement.

If the plot exhibits marked downward curvature at high Fcalc, it may be necessary to apply an extinction correction by ticking the EXTI box in the Refine tool panel and refining the model again.
I/sigma vs resolution
The quality of the diffraction data may be evaluated with this graph. I/σ is plotted as the larger green and red squares (green if I/σ ≥ 3σ, red otherwise) and the cumulative number of unique reflections is plotted as the smaller grey squares. It is, of course, desirable to have high I/σ out to high 2θ. However, in practice, it is optimal to have I/σ > 3 at least out to the 2θ value recommended by the IUCr, in order to ensure that the structure can be determined at an accepted minimum resolution.
cc half vs resolution
This graph plots the Pearson's correlation coefficient between random half data sets, CC1/2, as a function of resolution. Essentially, this method tests how well one half of the data predicts the other half, and constitutes a measure of the "resolution" of the data set as a whole. The coefficient CC1/2 is generally close to 1 at low resolution (low 2θ) and tapers off somewhat at high resolution (high 2θ).
Rmerge vs resolution
Rmerge measures how well multiple measurements of the same reflection agree. Rmerge is plotted as the larger green and red squares (green if Rmerge ≤ 0.15, red otherwise) and the cumulative number of unique reflections is plotted as the smaller grey squares. Data corresponding to an Rmerge above 0.15 are considered of questionable value. It is optimal to collect data with an Rmerge < 0.15 out to at least the IUCr-recommended resolution limit.
Fobs over Fcalc
Ideally, Fcalc ought to be as close as possible to Fobs at the conclusion of refinement, i.e., their ratio is expected to be close to unity. Therefore, this ratio plotted here as a function of resolution is expected to be close to 1 throughout, though deviations may be observed at high resolution. To prevent division of the diffraction into data bins and plot Fobs/Fcalc for individual reflections, untick the Binning box.
Completeness
Plots percent completeness (Laue completeness and point group completeness) of the diffraction data against resolution. Good data will show nearly 100% completeness over the entire resolution range.
Normal probability
This plots the ordered weighted deviations, w(Fobs2 - k * Fcalc2), against the deviations that would be expected if the errors in the data were normally distributed. If the errors are in fact normally distributed, this plot will be linear with slope 1 and intercept 0. Significant departures from this ideal may indicate problems with the diffraction data, model, or weighting scheme.
Fractal dimension
This plot ideally appears as a symmetric, inverted parabola, but noise in the data or systematic errors cause deviations from this parabolic shape. The narrower the curve, the flatter the residual electron density distribution; minimum and maximum values of the residual electron density appear as the left and right x-intercepts of the plot, respectively. For more information on this plot, see K. Meindl & J. Henn, Acta Cryst. A64, 404 (2008).

Note: This plot takes a little longer to generate than the others.
Scale factor vs resolution
The scale factor should be approximately constant at 1 across the whole data range if the diffraction data are good. A low value of the scale factor at high values of 2θ may indicate that high-angle data are weak or absent.
R1 factor vs resolution
The value of R1 increases gradually with increasing 2θ. Sudden changes in R1 indicate problems with the diffraction data.
Bijvoet Differences Probability Plot
This is a plot of the deviations in the observed vs calculated Bijvoet differences, analogous to the Normal probability plot above. This plot frequently deviates from linearity, indicating that the experimental errors are not normally distributed. Hooft et al. (J. Appl. Cryst. 43, 665 (2010)) have suggested that a Student's "t" distribution may better describe the errors in the Bijvoet differences, especially if the data quality is poor. By default, the plot is generated assuming that the errors obey a normal (Gaussian) distribution. Tick the Student's t box to redraw the plot using the Student's "t" distribution instead. A comparison of the two types of plots allows the determination of the most appropriate distribution for the errors in the data.
Bijvoet Differences Scatter Plot
The observed Bijvoet differences, ΔFobs2 = Fobs2(+) - Fobs2(-), are plotted here against the calculated Bijvoet differences ΔFcalc2 = Fcalc2(+) - Fcalc2(-), with error bars indicating the uncertainty in the observed Bijvoet differences. For a correctly determined absolute structure, this graph has a positive slope close to 1. As with the Bijvoet Differences Probability Plot above, the graph can be created using either the normal distribution (default) or the Student's "t" distribution (by ticking the Student's t box). A negative slope for this plot may indicate incorrect assignment of the absolute structure, which may need to be inverted with the following command:
$+ html.Snippet(GetVar(default_link),"value=inv -f","hint=inv -f","onclick=inv -f","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Invert the current structure (the '-f' switch forces the inversion).

REFLECTION-STATISTICS-SUMMARY-HELP

REFLECTION_STATISTICS_SUMMARY

This table collects in one place the most important indicators of the quality of the diffraction data used for refinement. These parameters are independent of any structure model or refinement process.
TotalReflections
Total number of reflections recorded during the diffraction experiment.
UniqueReflections
Total number of unique reflections (unrelated by symmetry) recorded during the diffraction experiment.
DataCount
Equal to the number of unique reflections, above.
FriedelOppositesMerged
A "1" here indicates that Friedel reflection pairs (h, k, l) and (-h, -k, -l) in the data were merged, and a "0" means none were merged.
InconsistentEquivalents
Number of pairs of equivalent reflections that are dissimilar in the data set.
SystematicAbsencesRemoved
Total number of systematically absent reflections that were removed from the data set.
MinD
Minimum resolution of the data set, in Å.
MaxD
Maximum resolution of the data set, in Å.
LimDmin
Minimum possible resolution (theoretical limit based on the unit cell dimensions), in Å. This value may be higher than the theoretical limit due to SHEL or ranged OMIT commands (e.g., "SHEL 15 0.8" or "OMIT -3 50") applied to the data.
LimDmax
Maximum possible resolution, in Å. This value may be affected by SHEL or ranged OMIT commands (e.g., "SHEL 15 0.8" or "OMIT -3 50") applied to the data.
FilteredOff
Number of reflections removed from the data by SHEL or ranged OMIT commands (e.g., "SHEL 15 0.8" or "OMIT -3 50").
OmittedByUser
Number of reflections omitted from the data by specific OMIT commands such as "OMIT 1 0 0".
OmittedReflections
Number of reflections removed from the data set and placed after the (h, k, l) = (0, 0, 0) line in the .hkl file.
IntensityTransformed
Number of reflections whose intensities have been transformed by an "OMIT s" command, i.e., whose Fobs2 has been replaced by 0.5sσ(Fobs2) throughout the data set.
Rint
A measure of the precision with which individual reflections were measured in the diffraction experiment. If Rint is about two to three times bigger than Rsigma (see below), there may be a problem with the data set.
Rsigma
A measure of the signal-to-noise ratio in the diffraction experiment.
MeanIOverSigma
Average value of I/σ(I) over the entire data set; a measure of the signal-to-noise ratio in the diffraction experiment.
Completeness
Point group completeness of the data set out to the maximum 2θ recorded in the diffraction experiment.
MaxIndices
Maximum values of the indices h, k, and l in the data set used for refinement (i.e., after OMIT statements have been applied).
MinIndices
Minimum values of the indices h, k, and l in the data set used for refinement (i.e., after OMIT statements have been applied).
FileMaxIndices
Maximum values of the indices h, k, and l in the data set, as originally recorded in the diffraction experiment.
FileMinIndices
Minimum values of the indices h, k, and l in the data set, as originally recorded in the diffraction experiment.
ReflectionAPotMax
Maximum redundancy of a reflection in the data set (counting symmetry-equivalent reflections).
FriedelPairCount
Number of Friedel pairs (h, k, l) and (-h, -k, -l) measured (in P1) in the data set.
Redundancy
In the set of numbers (n1, n2, n3, ...) listed here, n1 is the number of reflections in the data set measured once, n2 is the number of reflections measured twice, n3 is the number measured three times, etc.
IsCentrosymmetric
This number is 1 if the structure is centrosymmetric and 0 if it is non-centrosymmetric.
Completeness_laue_full
Laue group completeness of the data set, calculated out to the IUCr-recommended resolution limit sin(θ)/λ ≥ 0.6 (e.g., 2θ ≥ 50.5° for Mo Kα radiation).
Completeness_point_full
Point group completeness of the data set, calculated out to the IUCr-recommended resolution limit sin(θ)/λ ≥ 0.6 (e.g., 2θ ≥ 50.5° for Mo Kα radiation).
Completeness_laue_max
Laue group completeness of the data set, calculated out to the maximum 2θ recorded in the diffraction experiment.
Completeness_point_max
Point group completeness of the data set, calculated out to the maximum 2θ recorded in the diffraction experiment.

ELEMENTAL_ANALYSIS

Elemental analysis, molar mass and simulated mass spectrum.
Elemental Analysis: CHN
Click this button to calculate the expected values of a CHN analysis from the structure model. The molar mass (molecular weight) in g/mol and a full elemental analysis are also provided. The equivalent line command is 'calcCHN'.
Calculate Molecular Isotope Pattern: Mass Spec
Calculates a simulated molecular isotope pattern for the structure using the natural abundances of all isotopes. Equivalent to typing 'calcms' at the command prompt.

MOLECULAR_VOLUME

Total molecular volume and polyhedral volume of individual atoms.
Molecular Volume
Calculates the total molecular surface area in Å2 and molecular volume in Å3. The line command is ' vvol'.
Calculate Polyhedral Volume
Calculates the volume of a polyhedron defined by the selected atom (line command 'calcvol').

R_S_CHIRALITY_DESIGNATIONS

These tools enable the analysis of chiral carbons in a structure.
List R/S Designations of Chiral Carbons
Clicking this button prints a list of all the chiral carbons in the asymmetric unit along with the R/S configuration of each. The equivalent line command is 'rsa'.
Label Chiral Carbons as R/S
Click this button to label each chiral carbon on the screen with its respective R or S configuration.

BOUNDING_BOX_AND_GEOMETRY_INDEX

Display a rectangular bounding box or calculate a geometry index.
Molecular Bounding Box
Click this button (or type 'wbox') to display a rectangular box surrounding the structure on the screen. The structure will be shown in space-filling view, and the dimensions and volume of the box will be printed on the screen. To remove the box, right-click on it with the mouse and select Hide. To return to a ball-and-stick view of the structure, type 'pers'.
Geometry Index
For 4-coordinate and 5-coordinate geometries, this will calculate the Geometry Index of the central atom . The procedure and relevant citations can be found in the linked Wikipedia article.

4-coordinate:  A parameter τ4 is calculated from the bond angles about a selected tetracoordinate atom. This parameter provides a measure of whether the geometry around the selected atom is square planar (τ4 = 0) or tetrahedral (τ4 = 1).

An additional parameter τ4' is also calculated, which will always be less than or equal to τ4. The parameter τ4' is also 0 for square planar geometry and 1 for tetrahedral geometry. However, τ4' can be used to distinguish other forms besides the square planar and tetrahedral geometries, such as the seesaw geometry, for which τ4 ≈ 0.43 and τ4' ≈ 0.24.

5-coordinate:  A parameter τ5 is calculated from the bond angles about a selected pentacoordinate atom, which measures whether the geometry around that atom is square pyramidal (τ5 = 0) or trigonal bipyramidal (τ5 = 1).

FRAGMENT_LIBRARY

Clicking this link opens Ilia Guzei's Idealized Molecular Geometry Library (IMGL) in your default internet browser. Fragments contained in this library can be copied and pasted straight from the web site into Olex2. Simply copy the desired fragment atomic coordinates, including the FRAG and FEND lines, from the IMGL web site and paste them directly into the command line to insert the fragment into the structure. Detailed, step-by-step instructions, with examples, for this process are found in Ilia Guzei's Manual linked on the Olex2 Home tab. For more information on the FRAG command, consult the ShelX Manual.

Note: No constraints, restraints, or occupancies will be applied to the pasted fragment! These will have to be entered separately.
Pasted fragments
The inserted fragments will appear in a slightly greenish colour on the screen while in the matching mode. Fragments can be matched to electron density peaks by first clicking on an atom in the imported fragment and then on the corresponding Q-peak, then repeating the process with other atom/Q pairs until the fragment is in the desired position and orientation.
Exit matching mode
Press 'Esc' repeatedly, click the Esc link in the orange mode box, or type 'mode off' to exit the matching mode.

LINK_SELECTED

Select two atoms to be "linked" in the refinement, as described below.
Occupancies
Clicking Occupancies links the occupancies of the two atoms to one another so that the individual occupancies add up to unity. This is also accomplished by the ' fvar sel' command.
Parts and Occupancies
The occupancies will be linked such that the individual occupancies add up to unity, as above, and the selected atoms will be added to different PARTs as well. Equivalent to the line command 'part -p=2 -lo sel'. Here, the "-p=2" switch dictates that the atoms should be assigned to two PARTs, and "-lo" stands for "link occupancy".

LINK_CONSTRAINTS

Link PARTs and occupancies of selected atoms, then apply either an EADP constraint or an ISOR restraint to them.

LINK_PARTS_1

Assign the selected atoms to the PART number in the scroll box at the end of this line.

LINK_PARTS_2

Assign the selected atoms to two PART numbers, in order.

SHOW_PARTS

If a structure contains atoms that have been assigned to PARTs, then it is sometimes useful only to display atoms belonging to certain PARTs.
$+ html.Snippet(GetVar(default_link),"value=showP 0 1","hint=showP 0 1","onclick=showP 0 1","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show only atoms belonging to PARTs 0 and 1.
$+ html.Snippet(GetVar(default_link),"value=showP 0 2","hint=showP 0 2","onclick=showP 0 2","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show only atoms belonging to PARTs 0 and 2.
$+ html.Snippet(GetVar(default_link),"value=showP 0 -1","hint=showP 0 -1","onclick=showP 0 -1","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show only atoms belonging to PARTs 0 and -1.
$+ html.Snippet(GetVar(default_link),"value=showP 0 -2","hint=showP 0 -2","onclick=showP 0 -2","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show only atoms belonging to PARTs 0 and -2.
$+ html.Snippet(GetVar(default_link),"value=showP 1 2","hint=showP 1 2","onclick=showP 1 2","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show only atoms belonging to PARTs 1 and 2.
$+ html.Snippet(GetVar(default_link),"value=showP 1","hint=showP 1","onclick=showP 1","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show only atoms belonging to PART 1.
$+ html.Snippet(GetVar(default_link),"value=showP 2","hint=showP 2","onclick=showP 2","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show only atoms belonging to PART 2.
$+ html.Snippet(GetVar(default_link),"value=showP","hint=showP","onclick=showP","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will show all atoms in all PARTs.

SPLIT_GROUP

The tools on this line will fully split each of the next atom(s) clicked into two atoms.
Split
When this button is clicked, Olex2 will enter a mode in which each atom clicked will generate two atoms (at the focal points of the ellipsoids). The occupancy of each split atom will be set initially to 0.5; one of the atoms will be in PART 1, the other in PART 2. After the splitting has occurred, the newly "generated" atoms can be moved to any desired location by holding the 'SHIFT' key and dragging each one with the mouse. The line command for the Split tool is 'mode split'. Press 'ESC' to exit the mode.
EADP
This will split the atom(s) as above, but will constrain the ADPs for both atoms to be the same. This is useful in early stages of refinement, but should probably be removed once the disorder model is nearly complete, preferably applying a DELU restraint instead. This corresponds to the line command 'mode split -r=EADP'.
ISOR
This will split the atom(s) as above, and apply an ISOR restraint to each of the two atoms. The equivalent line command is 'mode split -r=ISOR'.
SIMU
As above, but with a SIMU restraint. The line command for this function is 'mode split -r=SIMU'.

FOLDER-VIEW-HELP

FOLDER_VIEW

Click Select a folder to choose the parent folder containing data files for all structures. A tree view of all subfolders will appear here, simplifying browsing for structures in the future.

HAR_REFINEMENT

HAR is super.

HFIX_QUICKMODES

This tool tab contains common constraints relevant to hydrogen atom placement. Hover over each little symbol to display the ShelX constraint that will be applied to the selected atom(s). When one of the symbols is clicked, Olex2 will enter a mode for the application of that particular constraint. Click on the atom(s) to which the constraint is to be applied, then press 'ESC' to exit the mode. It is also possible simply to type the code for the constraint after selecting an atom.

TOOLBAR_HYDROGEN_2

This tool tab provides methods of adding H atoms to the structure with custom X-H bond distances.
A, D, and HFIX
Type the desired AFIX code into the A box, the desired X-H bond length (in Å) into the D box, and click HFIX. This will enter a mode in which this constraint is applied to any atom(s) clicked (hydrogen atoms will be placed geometrically on the clicked atoms). Press 'ESC' to exit the mode.
H 'Improve'
This feature is taken straight from the syntax of the crystallography graphics program XP. The distances provided in the HIMP drop-down menu are typical X-H bond distances observed by neutron diffraction. Selecting a bond distance from this menu enters a mode for assigning this bond distance to X-H bonds. Alternatively, typing a value into the HIMP box and pressing ' TAB' also enters the mode. Once in the mode, clicking a hydrogen atom will move it along its X-H bond axis to the distance specified in the HIMP box.
$+ html.Snippet(GetVar(default_link),"value=himp 0.983","hint=himp 0.983","onclick=himp 0.983","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This will set all X-H bonds in the structure to 0.983 Å.

TOOLBAR_HYDROGEN_3


Add Hydrogen
Clicking this link will place hydrogen atoms geometrically throughout the structure and constrain them according to their respective environments (sp2, sp3, etc.). To refine any hydrogen atom positions freely, select the atom(s) to which the hydrogens are bonded, type ' AFIX 0', then refine again.
H Labels
Will display the names of all atoms, including hydrogen atoms.
$+ html.Snippet(GetVar(default_link),"value=labels -h -l","hint=labels -h -l","onclick=labels -h -l","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Show all atom names, including hydrogen atom names.

No H Labels
Displays the names of all non-hydrogen atoms.
$+ html.Snippet(GetVar(default_link),"value=labels -l","hint=labels -l","onclick=labels -l","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Show all non-hydrogen atom names.

Show AFIX
Displays the AFIX code (if any) on each hydrogen atom in the structure.
$+ html.Snippet(GetVar(default_link),"value=labels -h -a","hint=labels -h -a","onclick=labels -h -a","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This shows the AFIX constraint code for each hydrogen in the structure.

FREE ALL H
Removes all AFIX constraints from all hydrogen atoms, and also frees their Uiso values, so that they can be freely refined.
Hide Q
Hides all electron density peaks (Q peaks) on the screen.

HTAB_SLIDER

The 'htab' instruction provides an analysis of hydrogen bonding in the structure. It can only be used when the asymmetric unit alone is on the screen, but hydrogen bonds to symmetry-equivalent atoms will be shown. The list of hydrogen bonds matching the criteria set by the sliders below is printed in the graphics window.
Distance
This slider specifies the maximum D-A distance (in Å) for a D-H···A interaction in the structure to be counted as a hydrogen bond.
Angle
This slider specifies the minimum D-H-A angle (in degrees) for a D-H···A interaction in the structure to be counted as a hydrogen bond.

HYDROGEN_BOND_SLIDER

Slide this indicator to the right to enter a mode showing potential hydrogen bonding interactions at increasingly longer distances. Clicking on any of the broken-line "bonds" growing from an atom will display the portion of the structure to which that atom is hydrogen bonded. Press 'ESC' to exit the mode.

IMAGES

Olex2 can export images of a structure in a variety of formats, with many options available in this tool tab. Atoms are also labelled using the tools here.
File name and format
Enter a name for the image file here or use the default file name provided. Options for dealing with duplicate picture file names are specified here as well. The Default file format for saved images is bitmap, but other formats may be selected from this drop-down menu.
Atomic Labels
This attaches customisable labels to individual atoms in the structure. These labels are distinct from the ordinary names given to atoms during refinement or defined with the Naming tool tab under Refine. The selected button only labels those atoms highlighted in the graphics window, non-H labels all non-hydrogen atoms, and hetero labels all atoms other than carbon and hydrogen. To label all atoms, type 'sel atoms' at the command line to select all atoms and click the selected button.
Symmetry label and Style
The Symmetry label drop-down menu offers several options for attaching a descriptive suffix to the labels of atoms related by symmetry to those in the asymmetric unit. The Style drop-down menu allows the user to select from a couple of different options for formatting that portion of the atomic label which follows the element symbol.
Moving and Deleting Labels
Hold down the 'Shift' key and drag a label with the left mouse button to move it. To delete a label, first make sure no atoms, bonds, etc. are highlighted (hit ''Esc' to deselect all). Left-click the label(s) to be deleted and hit the 'Delete' key. To select all labels, click on any one label and then press 'CTRL+A'. To delete all atomic labels, click the DELETE all labels link.
Label Colour and Label Box
To alter the colour and appearance of atomic labels, click the Choose the label colour link to open a menu for customising a label's colour properties. Click the Label Box link to customise the properties of the bounding box enclosing each atomic label.
Align and Lock


View and Plane:  Clicking on one of these links will orient and centre the structure within the display window, which can be useful before creating images. View centres and orients a structure on the screen using an algorithm involving the calculation of the structure's principal axes of inertia. Plane calculates a mean plane through the entire structure, orients the structure on the screen perpendicular to this plane, and centres the structure on the screen. Neither of these methods changes the zoom level. Typing 'mpln -r' displays the mean plane and prints its equation in the output window. To delete the plane, click on it and press 'Delete'.

A couple of other helpful line commands for realigning the structure on the screen are:
$+ html.Snippet(GetVar(default_link),"value=center","hint=center","onclick=center","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Centres the structure without changing orientation or zoom level
$+ html.Snippet(GetVar(default_link),"value=compaq -a","hint=compaq -a","onclick=compaq -a","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Also centres the structure without changing orientation but does resize the structure to fit within the display area.


Note: The atom legend can be moved to any desired location on the screen, e.g., closer to the structure, by holding down the 'Shift' key and dragging it with the mouse. The legend display can also be switched off or on with the 'legend' line command. To reset the legend (e.g., if it has disappeared), type 'legend -r'.

Lock:  When working with images, it is sometimes helpful to lock out certain mouse functions to avoid accidentally changing the orientation or zoom. The zoom, rotation, and translation functions may be individually locked by ticking the appropriate box. For example, if only the Translation box is ticked, the structure will remain in a fixed location on the screen, but it will still be possible to rotate it or to zoom in and out. All three functions may be locked simultaneously by ticking the Lock all box.

BITMAP_IMAGES

Olex2 can produce bitmap images of structures in a variety of formats, with no limit on the image file size. All images produced are in the RGB colour space. If CMYK images are required, e.g., for publication, a separate RGB-to-CMYK conversion tool will be needed. Many such image conversion tools are available on the internet, where an uploaded RGB file is received back as a CMYK file.

BITMAP_IMAGE_ATTRIBUTES


File Format
Select a format, such as .png or .jpg, for the image file from this drop-down menu. The default format is .png (recommended), which involves lossless compression of images and results in relatively small files.
Transparency
It is possible to set the background for the structure to be transparent, but this will cause purely white parts of the structure also to become transparent. To work around this, set the background of the image to some colour that does not occur in the structure (pink is usually a good choice). Then, convert all pixels of that colour to a transparent background using PowerPoint or other graphics software. There are many ways to achieve a transparent background using professional image processing software.
Make Image
Click the Go! button to save an image of the structure in the current working folder. The image will not contain any displayed text besides atomic labels and the legend. However, the current background will be part of the image. To change to a plain white background, press 'F2' once or twice.

BITMAP_IMAGE_ATTRIBUTES1


Resolution
Set the image resolution in DPI from the drop-down menu or type in a custom value.
Width
Set the image width in inches or centimetres from the drop-down value or enter a custom width into this box. The image width in pixels will be automatically adjusted, depending on the resolution selected.
Size
Select a value from the Size (px) drop-down menu to specify the image width in pixels. The width of the image will automatically be adjusted depending on the resolution selected. It is also possible to type in a custom value into the Size (px) box. If the value is 100 or greater, it is interpreted as the width of the image in pixels; if it is less than 100, it is interpreted as a percentage of the display size. Thus, entering 1000 in the Size (px) box will generate an image 1000 pixels wide, but entering 85 will generate an image with a size 0.85 times the display area. There is no limit on the size of the bitmap file created.
$+ html.Snippet(GetVar(default_link),"value=pict molecule.png 300","hint=pict molecule.png 300","onclick=pict molecule.png 300","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Creates a PNG image file called molecule.png in the working folder with a width of 300 pixels.

BITMAP_IMAGE_TRIM


Trim
Ticking this box adds the specified padding and border to the image. Custom values can be entered in all the drop-down menus described below.

Padding:  Adds a white padding around the image of the specified percent thickness.

Border:  Adds to the image a border of the thickness specified in the Border (%) drop-down menu and of the colour specified by the hexadecimal code in the Colour dropdown menu. The color corresponding to the hexadecimal code is displayed in the square box next to the Colour menu.

BITMAP_ATOM_LABEL_FONTS



Note: This section pertains to user-defined atom labels created in the Images tool tab above, not to atom names generated during refinement or defined using the Naming tool tab under Refine.

Set the fonts for atom labels and bond labels here. Click the Atom Label Font (Olex2) link to change the settings of the default Olex2 font used for atom labels. To use a system-supplied font such as Courier or Arial for labels instead of the built-in Olex2 font, click the adjacent (System Font) link and select the desired font from the menu that appears. Similarly, click Bond Label Font (Olex2) to change the settings of the default Olex2 font used for bond labels, and on its adjacent (System Font) link to use a system-supplied fonts for bond labels.

POSTSCRIPT_IMAGES

Some would argue that there is no better way to represent a crystal structure on paper than a clear black-and-white ORTEP drawing. Such drawings can be made using Olex2. There are very many different options for generating ORTEP-style drawings. Many of these can be set from this GUI, but for more exotic options, please consult the Olex2 manual in the Start tool tab under Home.

PS_ROW_1

Tick the Coloured Atoms and Coloured Bonds boxes to show atom outlines and bonds, respectively, in colour. If the Filled Atoms box is ticked, all coloured atoms will be drawn filled with their respective colours. Tick the Pers box for a perspective view of the structure.

Once all the PostScript graphics options are set, click the Go! button to create a .ps image file in the working folder.

PS_ROW_2

Set the atom outline and octant line widths from these drop-down menus.

PS_ROW_3

Specify the number of sections into which each octant face is to be divided and the width of the octant divider lines using the drop-down menus here.

PS_ROW_4

Set the width of bonds to hydrogen atoms here as a fraction of the normal bond width. The width of all other bonds is controlled with the Bond r slider in the Quick Drawing Styles tool tab under View, or with the 'brad' line command.

PS_ROW_5

The thickness of the font and the font size used for atom and bond labels are set from these drop-down menus. A greater font thickness will make the font appear more bold.

PS_ROW_6

Adjust the size of the bond font using this drop-down menu.

PS_ROW_7

By default, hydrogen atoms placed in riding positions and displayed as uniform spheres will not have octants cut out. Carbon atoms will also not have octants cut out because of the -\$C instruction included by default on this line. All other atoms will be displayed with cut-out octants by default. Select the +\$C option from this drop-down menu to show carbons with octants cut out as well.

POVRAY_IMAGES

It is possible to export a structure in the popular POVRAY format as a 3D object. POVRAY is capable of generating sophisticated images with rendered shadows and backgrounds, as well as 3D animations, but this requires in-depth knowledge of POVRAY techniques. There are no options here, as Olex2 merely creates a .pov image file for further elaboration with POVRAY tools.
$+ html.Snippet(GetVar(default_link),"value=pictPR filename.pov","hint=pictPR filename.pov","onclick=pictPR filename.pov","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Saves the POVRAY output file 'filename.pov'.

PR_ROW_1

Click the Go! button to create a POVRAY image in the current working folder.

IMAGE_SERIES

Creates a series of bitmap images of the structure rotating about the x, y, or z axis.

IS_ROW_1

Click the GO button to create a series of still images of the rotating structure. The images, numbered 000, 001, 002, etc. will be stored in a folder called movie in the current working folder. The images can be concatenated in sequence to create an animation of the structure rotating.

IS_ROW_2

The Rotation around Axis box specifies the axis of rotation (1 = x, 2 = y, and 3 = z). Degree specifies the number of degrees by which the structure is to be rotated before each subsequent image in the series is captured.

IS_ROW_3

Number of Frames specifies the number of still images to be captured, and Size determines the size of each image in the series.

MAP_VIEW


Available Display Modes
The plane, contour, surface, wire, and points options shown under the View drop-down menu are different viewing styles available for displaying maps and masks in Olex2.

plane, contour, contour+plane:  These three views show an interactive 2D slice of a map, i.e., a display of a parameter such as the calculated electron density, in the plane of the screen. The structure can be rotated, moved or zoomed while the map is displayed, and the 2D slice will change accordingly as different portions of the structure pass through the plane.

Colours:  Select the number of colours in the colour scale of a 2D map display in plane and contour+plane modes from this drop-down menu.

surface, wire, points:  These three views show a 3D display of a parameter, such as the calculated electron density, overlaid on the structure. If there is insufficient electron density, however, only the 2D display will the shown. If the computer struggles to display these maps, first adjust the display levels in the points view, then select wire or surface, since the latter are more computationally demanding graphics displays.

In the surface, wire, and points display modes, positive values of electron density are shown in green and negative values (holes) in red, providing a very powerful tool for checking the validity of a structure during refinement. Thus, for example, if the diff (difference between Fobs and Fcalc) map for a structure is displayed in the wire view and a hydrogen atom is encased in a red blob, with a green blob nearby, then that hydrogen should probably be moved to the position of the green blob if the new position is chemically reasonable. A useful keyboard shortcut to display the diff map is 'CTRL+M'.

Extended:  Ticking this box will extend the map display out from one unit cell to 27 adjacent unit cells, a 3 x 3 x 3 stack. This is very useful for viewing the shapes, sizes, and distribution of voids in the structure.

Edit:  Click this button to edit the colour properties of the various map surfaces.

2D_MAP_CONTOURS

This slider selects either the maximum number of contour lines (for the contour and contour+plane view) or the number of colours (for the plane and contour+plane views). In contour view, regions of positive electron density are displayed as solid lines, whilst regions of negative electron density (holes) are displayed as dashed lines. A contour map will be included in any PostScript drawing created whilst the map is displayed.

Hint:  If symmetrical maps around 0 are desired, then select, e.g., 21 contours, giving 10 above 0, 10 below 0 and one for the 0 level itself.

2D_MAP_SCALE

This option sets the maximum and minimum of the electron density in a map. Clicking Automatic (the default setting) will adjust the map display so that the minimum and maximum on the map legend match the minimum and maximum electron density in the current map slice. Static, on the other hand, leaves these minimum and maximum values fixed at the global minimum and maximum, respectively, no matter what slice is currently shown.

2D_STATIC_MAP_SCALE


Min
Use this slider to define the minimum value of the parameter displayed on the map. The slider adjusts the minimum in quarter-integer values but also accepts manual input in the text box next to it.
Step
This slider defines the step size between two adjacent contours/colours. As with Min, this slider has pre-defined slider values (difference 0.02), but a specific value can also be typed into the text box.

2D_MAP_POSITION_AND_SIZE


Depth
This slider controls the depth of the map plane "into" the screen. More negative values of Depth move the map further into the screen until the map is "behind" the model. More positive values move the map further out of the screen until the map is "in front" of the model. Different parts of the structure will move through the 2D slice as Depth is changed. Alternatively, to move the map perpendicular to the screen (i.e., into or out of the screen), hold down the 'SHIFT' key while dragging the left mouse button in the map area. A little care must be taken to drag in an area of the map itself, not on the structure.

Select three or more atoms and click on the Depth button to align the map with the mean plane through the selected atoms. The mean plane will also be displayed; to remove it, left-click on it and press 'Delete'.
Size
The Size slider controls the size of the plotted map. Larger values will actually decrease the size of the map on the screen, but will increase the map resolution. The visible area of the map can also be adjusted by holding down the 'CTRL' key whilst dragging the right mouse button in the map area.

MAP_3D

The Level slider adjusts the level of detail desired in the displayed map. A value can also be entered into the box next to the slider. If the level is set high, only the most prominent features (i.e., biggest electron density peaks and holes) will be shown. If the level is low, on the other hand, many more peaks and holes will be displayed. Below a certain cutoff level, however, the features of the map become so overwhelmed by the noise in the data that the map becomes overcrowded and meaningless, besides being slow to display. To avoid this, the level will be locked at and below the cutoff level.

ELECTRON_DENSITY

This tool tab is for displaying various electron density maps. The specific parameter to be mapped is selected from the Map drop-down menu.
Map
Select from the drop-down menu the type of map to display.

diff:  Will display the difference map, Fobs-Fcalc. Make sure to select surface, wire, or points from the View drop-down menu under the Maps tool tab (accessed through Map Settings in this tool tab) for this map to be displayed correctly. The corresponding line command is 'CalcFourier -diff -r=0.1 -m' or simply 'CTRL+M'. This is an extremely important tool for checking the validity of a model. Red regions of the map represent areas of missing electron density and green regions represent areas of excess electron density.

fcalc:  Will display a map of the calculated electron density (Fcalc).

2Fo-Fc:  Will display the map of 2Fobs-Fcalc.

fobs:  Will display a map of the observed or experimentally measured electron density (Fobs).

fcfmc:  Will display the FCF Fc-Fc map.
Source
Select from this drop-down menu a data source to be used in constructing the map.
Res/Å
Type in the desired resolution (in Å) for the map.
Mask
If the Mask box is ticked, all electron density features (peaks or holes) near the structure on the screen will be displayed. If the box is left unticked, only electron density features within the unit cell will be displayed.
Show/Hide Map
Toggles the display of the map on the screen.

CALCULATE_VOIDS

Calculates the voids and channels in the structure, if present. This calculation uses the Olex2 internal libraries. For further information, type 'help calcvoid' or click the button below.
$+ html.Snippet(GetVar(default_link),"value=help calcvoid","hint=help calcvoid","onclick=help calcvoid","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Help entry for the 'calcvoid' command.

Resolution/Å
Specify the resolution of the void map here, in Å.
Distance/Å
Specify any additional distance (in Å) from the van der Waals surface at which the void space is to be calculated.
Precise
Tick this box for a more precise calculation of the voids in the structure.
Show/Hide Void
Toggles the display of the voids on the screen. A list of voids (if any) in the structure is also printed in the graphics window. When the Extended option at the top of this tool tab is checked, the voids are displayed in a 3 x 3 x 3 stack of adjacent unit cells, which can be helpful in visualizing void shapes.

CALCULATE_SOLVENT_ACCESSIBLE_VOIDS

This checks for the presence of voids in the structure large enough to hold a solvent. This calculation is based on the smtbx/cctbx Olex2 libraries, and provides an alternative algorithm to 'calcvoid' above for detecting voids in the structure. No map is produced, but a list of voids is printed in the graphics window.
Probe/Å
This adjusts the size (in &Aring) of a spherical "probe" that rolls about the structure, fitting into gaps and mapping out any cavities that may be present. A smaller sphere would fit into smaller gaps and therefore return a larger void size.
Grid/Å
This governs the resolution of the solvent void map. If the grid is set too high, the calculation will take a very long time, without producing a much improved map.
Show Info
A list of solvent-accessible voids (if any) in the structure is printed in the graphics window.

MASKS

The Masks tool tab offers an alternative to the well-known SQUEEZE  routine in Platon  for dealing with disordered solvent. Search online for "modelling solvent disorder" for more information. This sort of approach should only be used as a last resort when the solvent cannot be identified or modelled because of the severity of the disorder. Every effort should first be made to identify and model the solvent using the Disorder Tools in the Work tab and FragmentDB in the Tools tab. If refinement has been attempted using both ShelXL and olex2.refine, when the option appears to select either an olex or fcf file, ensure that the file from the last cycle of refinement is used.

See B. Rees et al., Acta Cryst. D61, 2005, 1299-1301 for more details on the algorithm used in this calculation.
Reflection File
Select a .hkl file for use in the calculation of the mask.
Use set completion
If low angle reflections are missing (even one is sometimes enough), the electron count in a cavity may be underestimated. If this option is selected, missing reflections are filled in and allowed to "float" throughout the Fourier transform iterations, resulting in more accurate estimates of the true electron count.
Show/Hide Void
Toggles the display of the voids on the screen. A list of voids (if any) in the structure is also printed in the graphics window. When the Extended option at the top of this tool tab is checked, the voids are displayed in a 3 x 3 x 3 stack of adjacent unit cells, which can be helpful in visualizing void shapes.
Map
Select mask from the Map drop-down menu to view the solvent-accessible voids in the structure. Selecting f_mask displays the Fourier transform of the solvent contribution to the structure factors. Lastly, selecting f_model displays the Fourier transform of the sum of contributions to the structure factors of both the solvent region and the ordered part of the structure.
Grid/Å
The Grid parameter is the resolution of the map, in Å. The entire structure, both atoms and solvent void regions, is divided into grid points given by this resolution in order to calculate the mask.
Solvent R in Å
All grid points at a distance greater than the sum of the van der Waals radius of an atom in the structure and Solvent R are initially set to be inside the solvent void region. The default value is 1.2 Å, which is large enough to avoid displaying voids in which no atom could fit.
Shrink truncation R in Å
After Solvent R above has been used to determine the solvent void region, all grid points outside this region are tested to see if they fall within a distance Shrink truncation R of the region. If this is the case, they are added to the solvent void region. Shrink truncation R is generally very close, or equal, to Solvent R. The process involving Shrink truncation R essentially results in a more close-fitting mask of the solvent void region.

MASKS-HELP



Select Volume:  A box with moveable sides will appear. Left-click on the coloured areas and then move the sides while pressing the SHIFT key. The map will be calculated only inside the defined box. You can delete the box by right-clicking on it and select 'Hide'.

OLEX2_RESTRAINTS_AND_CONSTRAINTS

This is a list of restraints and constraints specific to Olex2. These can be invoked when using the olex2.refine refinement engine.
RRINGS
Restrains all provided rings (e.g., C6, C5N, SC4) to be regular, i.e., flat with all interatomic distances similar.
TRIA
Restrains three atoms so that the distance between the central atom and the two specified bound atoms is the same. (Adds a distance restraint for the atom pairs and an "angle" restraint for the atom triplet.)
ADPUEQ
Restrains the ADPs of the selected atoms to the Ueq value provided. If no value is provided, the selected atoms will be restrained to be the same.
ADPVOL
The volumes of the ADP ellipsoids of the selected atoms will be restrained to be the same.
ANGLE
Applies a restraint to a bond angle. Select three atoms or two bonds to define an angle, then restrain the angle by typing 'restrain angle [value]' to [value] in degrees.
DIANG
Restrains a dihedral (torsion) angle. Select four atoms or three bonds to define a dihedral angle, then restrain the dihedral angle by typing 'restrain dihedral [value]' to [value] in degrees.

MATCH_1

This is a set of tools for matching fragments in the same structure or in two different structures. Please consult the online documentation linked in the Home tab for more information.
Match All Fragments
When the Match All Fragments link is clicked, Olex2 will automatically overlay any identical fragments currently displayed. These fragments may be in the same structure or in different structures (e.g., different CIF files) opened with the Overlay Structure tool below. The calculated RMS deviation for the matched fragments (overlaid with and without inversion) will be printed in the graphics window. The 'match' command can also be typed into the command line.
UnMatch
Click UnMatch to return to the unmatched fragments, or type 'fuse'.

MATCH_3

Select three atoms (say, A, B, and C) in the first fragment and then three atoms (say, X, Y, and Z) in the second fragment in the order they are to be matched (A to X, B to Y, and C to Z). Click Match Selected Atoms to overlay the fragments following the order of selection. To return to the unmatched structure click UnMatch or type ' fuse'.

MATCH_4


Overlay Structure
Clicking this link allows a second structure to be loaded; the current structure and the newly loaded structure will appear side-by-side on the screen in the Match mode. In this mode, clicking on an atom in the original structure and on an atom in the new structure superimposes the two structures. This process of clicking alternately on atoms in the first and second structures can be repeated to improve the alignment of the two structures (a total of three pairs of atoms can be selected). The first pair of atoms selected is directly superimposed, selection of the second pair rotates a structure to minimize the distance between the atoms of the second pair, and selection of the third pair rotates a structure about the line formed by the first and second pair to minimize the distance between atoms of the third pair. The two overlaid structures will be shown with red and green bonds, so that they can be differentiated. Press 'Esc' to exit the mode, and type ' fuse' to return to normal bonds instead of red and green bonds in the structures.
Mode Match
Clicking this link enters the Match mode in which fragments in a single structure (or in two separate structures) can be superimposed. See Overlay Structure, above, for a detailed explanation of the matching process.
Remove Overlay
Removes the second structure that has been added through the Overlay Structure link.

PLATON

Select a Platon  routine to run from the menu at right. The Platon  software has to be installed and the PATH environment variable properly set for these routines to work. The Pton button will show at the top of the Olex2 GUI if Platon  has been correctly installed. See Ilia Guzei's Manual linked in the Home tab for detailed instructions on installing Platon  for Olex2. For instructions on how to use a specific Platon  routine, please refer to the Platon web page.

SHELX_CONSTRAINTS

These are ShelX constraints. All of these will also apply to a refinement with olex2.refine.
AFIX
The AFIX instruction is for placing hydrogen atoms in idealized (riding) positions.
EXYZ
The EXYZ instruction is for specifying that two or more atoms share the same x, y, and z coordinates.
EADP
Specifies that the same anisotropic displacement parameters are to be used for two or more atoms, e.g., the three fluorines of a CF3 group.

AFIX

AFIX instructions are for placing hydrogen atoms in idealized (riding) positions in a structure.
Syntax of the AFIX command
Usage: AFIX mn d[number] sof[11] U[10.08]

From the ShelX manual:
"AFIX applies constraints and/or generates idealized coordinates for all atoms until the next AFIX instruction is read. The digits mn of the AFIX code control two logically quite separate operations. m refers to geometrical operations which are performed before the first refinement cycle (hydrogen atoms are idealized before every cycle), and n sets up constraints which are applied throughout the least-squares refinement. n is always a single digit; m may be two, one or zero digits (the last corresponds to m = 0)."

For more details, refer to the ShelX Manual.
Number drop-down menus
In this row, the first two drop-down menus after the constraint menu refer to m and n, respectively, in the AFIX command.
clear
Select any atom(s) to which an AFIX command has been applied. Clicking clear will remove the AFIX command.
de
Click de to enter a mode in which all AFIX instructions being applied to the structure are displayed. Also in this mode, the AFIX command currently specified in this tool tab can be applied to individual atoms by clicking on them.
go
Click go to apply the AFIX command currently specified in this tool tab.

EXYZ

Usage: EXYZ atomnames

This command imposes the same x, y, and z coordinates on all the named atoms (used when two or more elements share the same site in a structure, as commonly occurs in minerals). Often combined with EADP. The coordinates (and possibly free variable references as well) are taken from the first named atom in the list. An atom must not appear in more than one EXYZ instruction.

EADP

Usage: EADP atomnames

From the ShelX manual:
"The same isotropic or anisotropic displacement parameters are used for all the named atoms. The displacement parameters (and possibly free variable references) are taken from the first atom in the atom list that is linked to other atoms by EADP. The actual values, free variable references etc. given for the Uij of the other atoms are ignored. The atoms involved must either be all isotropic or all anisotropic. 'Opposite' fluorines of PF6 or disordered -CF3 groups are good candidates for EADP, e.g.

EADP F11 F14
EADP F12 F15
EADP F13 F16
C1 .......
PART 1
F11 ...... 21 ......
F12 ...... 21 ......
F13 ...... 21 ......
PART 2
F14 ...... -21 ......
F15 ...... -21 ......
F16 ...... -21 ......
PART 0

EADP applies an (exact) constraint. The SIMU instruction restrains the Uij components of neighboring atoms to be approximately equal with an appropriate (usually fairly large) esd."

For more details, refer to the ShelX Manual.

SHELX_RESTRAINTS

These are SHELX restraints. All of these will also apply to a refinement with olex2.refine. Click the go button to apply the restraint to the selected atom(s).

DFIX

Usage: DFIX d s[0.02] atom pair(s)
Restrains a distance d between pairs of atoms to a given value in Å within an estimated standard deviation of ± s (default 0.02 Å)

Example:   DFIX 1.54 0.01 C1 C2 C2 C3 C3 C4
Restrains the C-C bond distances of neighboring carbons in a butyl group to be 1.54 ± 0.01 Å, i.e., between 1.53 and 1.55 Å.

DANG

Usage: DANG d s[0.04] atom pairs
Restrains the "1,3 distance" or "angle distance" (distances between two atoms bound to a third, central atom) to a value d, within an estimated standard deviation of ± s (default 0.04 Å).

Example:   DANG 1.33 0.02 H1 H2
Restrains the H-H distance in a water molecule to be 1.33 ± 0.02 Å.

SADI

Usage: SADI s[0.02] atom pairs

Restrains bond lengths between given atom pairs to the same distance within an estimated standard deviation of ± s (default 0.02 Å).

Example:   SADI 0.005  C1 F1   C1 F2   C1 F3
Restrains a CF3 group to have the same C-F distances (within ±0.005 Å).

CHIV

Usage: CHIV V[0] s[0.1] atomnames

Restrains the "chiral volume" of the named atoms to a volume V Å3 within ± s Å. The "chiral volume" is the volume of the parallelepiped formed using as its edges the three shortest bonds from the named atom to exactly three other non-hydrogen atoms.

FLAT

Usage: FLAT s[0.1] four or more atoms

Restrains the named atoms to lie in a plane.

Example:   FLAT C1 C2 C3 C4 C5 C6 C7
Restrains the seven carbon atoms of a toluene molecule to lie in a plane.

DELU

Usage: DELU s1[0.01] s2[0.01] atomnames

Applies a "rigid-bond" restraint to the bonds in the list of named atoms. For adjacent atoms, this restrains the components of the anisotropic displacement parameters in the direction of the bond to be equal within ± s1 Å. A similar restraint is applied to 1,3 distances using s2.

SIMU

Usage: SIMU s[0.04] st[0.08] dmax[2.0] atomnames

Named atoms closer than dmax are restrained to have the same Uij components (anisotropic displacement parameters, ADPs) within ± s Å.

Example:   SIMU C1 C2 C3 O1
Restrains the ADPs of the atoms of an acetone molecule to be similar.

ISOR

Usage: ISOR s[0.1] st[0.2] atomnames

Restrains the Uij components of the named atoms to isotropic values within ± sst for terminal or isolated atoms). This restrained atoms will have approximately spherical ADPs. Useful for preventing atoms from having grossly misshapen ADPs or becoming non-positive definite (NPD), but not to be used indiscriminately.

Example:   ISOR C5 C6
This will restrain the ADPs of atoms C5 and C6 to appear approximately spherical.

RIGU

Usage: RIGU s1[0.004] s2[0.004] atomnames

Applies enhanced "rigid-bond" (see DELU above) restraints to bonds between adjacent atoms and to 1,3 distances with e.s.d.'s s1 and s2, respectively.

Example:   RIGU C1 Cl1 Cl2
Applies enhanced rigid-bond restraints to a dichloromethane molecule.

TWINNING-HELP

TWINNING

These tools provide methods of determining whether a structure is twinned, and if so, to calculate the twin law. The first two buttons on this row are for searching for twin laws, while the third button is to determine whether a structure is twinned.
Find 2-fold
Clicking Find 2-fold initiates a rapid search for 2-fold twin laws applicable to the structure. If a viable twin law is found, the corresponding transformation matrix will be printed in the output window. For example, suppose a 2-fold twin law is found with the following transformation matrix:

-1        0        0
0        -1        0
2/3      0        1

The twin law search will also suggest a BASF (batch scale factor, or fractional contribution of one of the twin components). If the suggested BASF is 0.204, entering the following two statements in the .ins file will take into account the observed twinning during subsequent refinement:

TWIN -1 0 0   0 -1 0   0.667 0 1   2
BASF 0.204

(The 2 at the end of the TWIN instruction is to specify a two-component twin.)
Find all Twinning
This searches for all twin laws applicable to the structure, not just the common 2-fold twin laws. If any are found, the corresponding transformation matrix and BASF will be printed at the bottom of this tool tab.
Cumulative Plot
Cumulative Plot opens the cumulative intensity distribution plot for the experimentally observed reflections. If the data points in the plot lie mostly along the bottom (red) line, the structure is very likely twinned.

GENERAL

This row contains the general settings that will be applied to all methods of searching for twin laws.
Extended
When this box is ticked, any twin law searches will be run in "extended" mode, i.e., more exhaustive (and therefore more time-consuming) searches will be performed. If no twin laws are found with this box unticked, then repeating the search with the box ticked may find a twin law missed by a normal search.
Min. Laws
The minimum number of viable twin laws to return. Setting a low number in this box speeds up the search, as the search terminates once the specified number of twin laws is found. However, they may be inferior to other applicable laws that may have been missed by setting Min. Laws too low. If the twin laws initially returned do not properly account for the twinning in the structure, increase this number and repeat the search.
Threshold for all searches
This threshold is the separation below which two points in reciprocal space (i.e., reflections) are considered to overlap. A larger value will suggest more potential twin laws for consideration, but may return laws that do not accurately describe the twinning in the structure; a smaller threshold will return fewer, more accurate laws.

SPHERICAL_ANGLE_AXIS

This tool tab offers two further ways to search for twin laws: Spherical and Angle-Axis.

The Spherical search method directly uses strong reflections, and the potential points they could map to on a sphere, to calculate viable twin laws for the structure. It is in general a faster search which searches less space whilst finding more laws, and is not restricted by the angle of rotation of the twin law. Spherical searching is strongly affected by the minimum law number, so if this search method yields poor results, increase Min. Laws and repeat the search.

The Angle-Axis search method, on the other hand, searches step-by-step for rotational twin laws by considering potential twin axes and rotations about them. Axes are taken from integer points in both direct and reciprocal space.

To try the first search method, first select the number of bad reflections to evaluate and then click Spherical. Specify Max Index and Rot. Fract'n, and click Angle-Axis to try the second.
Bad Refl'ns
Specify the number of bad reflections to use in the Spherical twin law search method. These are taken from the list in the Bad Reflections tool tab under the Info tab.
Spherical
Click this button to initiate a Spherical search for applicable twin laws.
Max index
This variable specifies the highest value of h, k, or l to use when searching for twin laws by the Angle-Axis method. A higher Max Index will find more twin laws, but the search will take longer.
Rot. Fract'n
The rotation fraction n governs the angle 360°/n, which is the step size of rotation about each axis during an Angle-Axis search. Increasing this variable will lead to finer steps and thereby to more twin laws.
Angle-Axis
Click this button to initiate an Angle-Axis search for applicable twin laws.

SET_HKLF5_REFLECTION_FILE

The HKLF5 file format is used exclusively for twinned structures, but is not always necessary if the structure is twinned. It is similar to the ordinary HKLF4 file format, but contains an additional data column identifying the twin component to which each reflection belongs. A file of this type is required for non-merohedral twinning, when the reciprocal lattices of the twin components cannot be exactly superimposed on one another.

GEOMETRY

Tools to analyse various geometrical parameters of a structure may be found here.

MEAN_PLANE_AND_BEST_LINE


Calculate Mean Plane
Select three or more atoms through which to construct a plane, then click this button or type 'mpln sel'. A best-fit plane through the selected atoms will be displayed along with the centroid of the plane. The output contains the equation for the plane and the hkl direction of the plane normal, as well as the RMS deviation (in Å) of the atomic positions from the plane. All symmetry-equivalent planes will automatically be added to any other fragments on the screen. To delete a plane, click on it and press 'Delete' (or hide it by right-clicking on the plane and choosing Hide from the Graphics submenu that appears). If all displayed planes are to be deleted, type 'sel planes' to select them all before pressing 'Delete'.
Calculate Best Line
Select two or more atoms through which a best-fit line is to be drawn. Clicking this button will calculate the best-fit line through the atoms and display it in a similar manner to a bond.

DISTANCES_AND_ANGLES


Distances and Angles
Displays the interatomic distance (for two selected atoms), the angle (for three selected atoms) or the torsion angle and tetrahedron volume (for four selected atoms) in the output window.

Note: For accurate e.s.d. values to be displayed for these parameters, a refinement must first be carried out with the Refine and Save e.s.d. Info button.
Refine and Save e.s.d. Info
Carries out a refinement to save the information needed to display accurate e.s.d. information for parameters such as bond lengths and bond angles.

ANALYSE_INTERACTIONS

Analyse non-bonding interactions in a structure.
π-π Interactions
Searches for π-π interactions in the structure; if any are found, the relevant geometric parameters (e.g., the distance between the centroids of adjacent aromatic rings) are printed in the output window.
Hydrogen Bonds
Finds and displays any hydrogen bonds in the structure. The equivalent line command is 'htab -g'. In both cases, a table is printed in the output window.

Another useful command for analysing nonbonding interactions is 'htab -t'. For example, 'htab -t=Br,I' would cause any Br---I halogen bonds in the structure to be displayed.

QUICK_DRAWING_STYLES

CELL-TARGET

Draw unit cell

BASE-TARGET

Display basis vectors

QUICK_DRAWING_STYLES

A number of preset drawing styles can be selected using the buttons in this tool tab. The new style will be applied only to the current selection. If no atoms are selected, the style will be applied to all atoms.
Balls & Sticks
$+ html.Snippet(GetVar(default_link),"value=pers","hint=pers","onclick=pers","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Atoms are shown as perfect spheres. The size of the sphere depends on the atomic radius of the element represented by the sphere.

Ellipsoids
$+ html.Snippet(GetVar(default_link),"value=telp 50","hint=telp 50","onclick=telp 50","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)") (n = 50 is the default )Anisotropic atoms are shown as ellipsoids. Isotropic atoms are shown as spheres, whose size depends on the Uiso value of the individual atom represented by the sphere.

Ellipsoids with hydrogen
Anisotropic atoms are shown as ellipsoids, and hydrogen atoms are shown as spheres with radii proportional to their respective Uiso values.
Wireframe
$+ html.Snippet(GetVar(default_link),"value=proj","hint=proj","onclick=proj","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")The structure model is shown as a wireframe.

Sphere Packing
$+ html.Snippet(GetVar(default_link),"value=sfil","hint=sfil","onclick=sfil","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Atoms are represented as space-filling spheres.

Tubes
$+ html.Snippet(GetVar(default_link),"value=tubes","hint=tubes","onclick=tubes","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")The entire model is represented as a set of connected tubes.

Polyhedra
$+ html.Snippet(GetVar(default_link),"value=mask atoms 37","hint=mask atoms 37","onclick=mask atoms 37","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows the structure in a polyhedral representation.

Def
$+ html.Snippet(GetVar(default_link),"value=default","hint=default","onclick=default","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")All display settings are reset to their default values.

Light
A display style showing carbon atoms in a light color against a dark background.

GRAPHICAL_OBJECTS

Several of tools are provided here to enhance the visualisation of a structure.
Cell
Toggles the display of the unit cell on or off.

Note: If the structure is not contained within the displayed unit cell, type 'move' to relocate it within the cell.
Base
Toggles the display of basis vectors.
Box Function 1
Toggles the display of a translucent box of the same size and shape as the unit cell. The box can be moved and rotated independent of the structure or the unit cell.
Box Function 2
Select two or more atoms. Clicking this button will toggle the display of a rectangular parallelepiped enclosing those atoms. This box can also be rotated and moved independent of the structure or the unit cell.

ALIGN_AND_LOCK


View and Plane
Clicking on one of these links will orient and centre the structure within the display window, which can be useful before creating images. View centres and orients a structure on the screen using an algorithm involving the calculation of the structure's principal axes of inertia. Plane calculates a mean plane through the entire structure, orients the structure on the screen perpendicular to this plane, and centres the structure on the screen. Neither of these methods changes the zoom level. Typing 'mpln -r' displays the mean plane and prints its equation in the output window. To delete the plane, click on it and press 'Delete'.

A couple of other helpful line commands for realigning the structure on the screen are:
$+ html.Snippet(GetVar(default_link),"value=center","hint=center","onclick=center","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Centres the structure without changing orientation or zoom level
$+ html.Snippet(GetVar(default_link),"value=compaq -a","hint=compaq -a","onclick=compaq -a","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Also centres the structure without changing orientation but does resize the structure to fit within the display area.

Lock
When working with images, it is sometimes helpful to lock out certain mouse functions to avoid accidentally changing the orientation or zoom. The zoom, rotation, and translation functions may be individually locked by ticking the appropriate box. For example, if only the Translation box is ticked, the structure will remain in a fixed location on the screen, but it will still be possible to rotate it or to zoom in and out. All three functions may be locked simultaneously by ticking the Lock all box.

LEGEND_SETTINGS

The default position of the legend (the atom types are represented by a sphere) can be set to be top/bottom and left/right -- and the padding from the edge of the display area can also be set.

Note: The atom legend can be moved to any desired location on the screen, e.g., closer to the structure, by holding down the 'Shift' key and dragging it with the mouse. The legend display can also be switched off or on with the 'legend' line command. To reset the legend (e.g., if it has disappeared), type 'legend -r'.

ADD_FOG

An artificial "fog" can be applied to the display by clicking the Add Fog button. This may be helpful, for example, to emphasise the 3D nature of the structure or to highlight its front-facing portion. The Front and Back sliders govern the thickness of the "fog". Click Clear Fog to remove the fog from the display.

ATOM_STYLES

The visual style of the atom display can be customised. Clicking on the link will display a Periodic Table, from where you can start customising your styles.
About Styles and Scenes
There are two types of style sheets in Olex2 - one deals with the atom objects (styles) and the other deals with the lighting and background settings (scene). Both have to be carefully tuned to each other in order to get good results. To load or save a style or scene, right-click on the background and then follow the relevant links.
Modify an Atom Style
Right-click on the atom, then select 'Graphics>Draw Styles'. The form you will see is quite complex, and you will have to experiment with it until you are familiar with what you can do.
Anisotropic Atoms
By default, the periodic table will open showing anisotropic atoms. Anisotropic atoms consist of the 'sphere' and the 'rims' - the visual properties of which can be set separately (see the drop-down box in the top right-hand corner of the 'Draw Styles' form).
Isotropic Atoms
When you see the periodic table, type the word 'pers' - and you will see a sphere representation of the atoms. You can now modify the settings for the isotropic view of atoms.

BONDS

TBI

ROTATE

Using these tools, a structure on the screen can be rotated in a more fine-grained and repeatable way than with the mouse.
Rotate about the x, y, or z axis
Enter the degrees of rotation into a Rotate box and click on one of the buttons on either side of the box to rotate the structure once in the negative or positive direction. Selecting x rotates the structure from bottom to top on the screen, y rotates from left to right and z rotates within the plane of the screen.

Using the 'rota' line command, even finer rotations by fractions of degrees are possible. Use '1' to stand for x, '2' for y, and '3' for z in the 'rota' command, e.g.,
$+ html.Snippet(GetVar(default_link),"value=rota 1 13.4","hint=rota 1 13.4","onclick=rota 1 13.4","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Rotate the structure around the x axis by 13.4°.
$+ html.Snippet(GetVar(default_link),"value=rota 2 -10.2","hint=rota 2 -10.2","onclick=rota 2 -10.2","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Rotate the structure around the y axis by -10.2°.

ANIMATE


Auto Rotation
Ticking a box in this tool tab continuously rotates the structure on the screen about the specified axis. A structure can be rotated simultaneously about more than one axis, and the speed of rotation can be set using the slider bar.

Clicking on a, b, or c resets the view to look down the chosen axis.

ZOOM

This slider enables zooming in or out on the structure displayed on the screen. The zoom can also be adjusted by holding down the right mouse button and moving the mouse. Click the Reset link or type 'gl.zoom' at the command prompt to return to a normal zoom level.

STEREO_VIEW

Depending on the hardware available, there are four options for obtaining a stereo view of a structure. There is also an option for viewing a structure in 3D without any special hardware at all. Click Normal View to return to the original 2D view on the screen in all cases. See the Olex2 3D View tutorial for more information, or search 3D viewing techniques online.
Stereo (Colour)
This mode is for viewing a structure using red/cyan 3D glasses. It results in a 3D structure displayed in grayscale (for colours matching those of the glasses). The 3D image is created by rendering two spatially separated projections.
Stereo (Anaglyph)
This mode is a different method for viewing a structure with red/cyan 3D glasses, and produces colour 3D images.
Stereo (Hardware)
Requires special hardware (3D monitor and accompanying 3D glasses) to view the 3D image.
Stereo (Interlaced)
As with Stereo (Hardware), this mode requires special hardware for viewing.
Normal View
Returns to the normal 2D display mode.
Viewing a structure in 3D without special equipment
It is possible to generate a 3D image that can be viewed using the "cross-eyed" method of the popular "Magic Eye" books, using no special equipment. Type 'gl.stereo(cross)' to generate the image. For best results, first resize the entire Olex2 window until the graphics display clearly shows both structures side by side within about a 10 cm x 10 cm square. Cross the eyes (or relax their focus as if staring off into the distance) to view the structure in 3D. The 3D image can be rotated, zoomed, and moved as usual.

SYMMETRY_TOOLS

This tool tab features a set of buttons for changing the appearance/location of the asymmetric unit; expanding ("growing") a structure on the screen; viewing the basis vectors and unit cell; and other similar tasks.

SYMMETRY_TOOLS_1

The tools in this row are useful for reorganising parts of a structure containing more than one moiety.
Move Near
This is useful for moving moieties of a structure close to a particular atom of interest.

  1. Click on an atom near which another moiety is to be moved.
  2. Activate the mode by clicking on the Move Near button (or typing 'mode move').
  3. Click on an atom of each moiety that is to be moved close to the initially selected atom.
$+ html.Snippet(GetVar(default_link),"value=mode move","hint=mode move","onclick=mode move","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")

Copy Near
This is a slightly different method for collecting moieties of a structure close to a particular atom of interest.

  1. Click on an atom near which another moiety is to be copied.
  2. Activate the mode by clicking on the Copy Near button (or typing 'mode move -c').
  3. Click on an atom of each moiety that is to be copied close to the initially selected atom.
$+ html.Snippet(GetVar(default_link),"value=mode move -c","hint=mode move -c","onclick=mode move -c","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")

Assemble
$+ html.Snippet(GetVar(default_link),"value=compaq","hint=compaq","onclick=compaq","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This command brings the various fragments of a structure as close together as possible on the screen.
$+ html.Snippet(GetVar(default_link),"value=compaq -a","hint=compaq -a","onclick=compaq -a","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Brings fragments of a structure together as above, but also assembles any "broken" fragments.

SYMMETRY_TOOLS_2

These buttons centre the moieties in a structure in different ways.
Centre on Cell
$+ html.Snippet(GetVar(default_link),"value=move","hint=move","onclick=move","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")All moieties in the structure will be centred within the cell.

Centre on Largest Part
$+ html.Snippet(GetVar(default_link),"value=move","hint=move","onclick=move","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")All moieties in the structure will be centred on the largest moiety.

SYMMETRY_TOOLS_3

These tools toggle the display of symmetry-related items on the screen.
Show Basis
$+ html.Snippet(GetVar(default_link),"value=basis","hint=basis","onclick=basis","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Displays/Hides the basis vectors of this structure.

Show Cell
$+ html.Snippet(GetVar(default_link),"value=cell","hint=cell","onclick=cell","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Displays/Hides the edges of the unit cell.

Quality
Use the slider to change the quality of the display graphics from low (far left) to medium (middle) to high (far right). A lower quality setting may be useful if the computer struggles to display large structures.
$+ html.Snippet(GetVar(default_link),"value=qual -l","hint=qual -l","onclick=qual -l","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)") , $+ html.Snippet(GetVar(default_link),"value=qual -m","hint=qual -m","onclick=qual -m","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)") , $+ html.Snippet(GetVar(default_link),"value=qual -h","hint=qual -h","onclick=qual -h","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Changes the quality of the display graphics to low, medium, or high.

SYMMETRY_TOOLS_4

These two important commands contract and expand the extent of the structure displayed on the screen.
Fuse
$+ html.Snippet(GetVar(default_link),"value=fuse","hint=fuse","onclick=fuse","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Display the asymmetric unit of the structure only. All symmetry-generated atoms will be removed. This is a command of fundamental importance.

Grow All
$+ html.Snippet(GetVar(default_link),"value=grow","hint=grow","onclick=grow","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")All symmetry-equivalent atoms required to show the "complete" structure will be displayed. In the case of polymeric structures, this is somewhat arbitrary, and more clearly defined 'grow' commands may need to be issued to display the structure as desired. See the Growing tool tab help for more options.

PACKING

This tool tab provides methods of visualizing the 3D packing of a structure.

EXPAND_SHORT_CONTACTS

Use this slider bar to define the minimum distance for interatomic "short contacts" such as hydrogen bonds or halogen bonds. As the slider moves to the right, more clickable "bonds" will be shown from atoms meeting the contact criterion. Alternatively, a number can be entered in the box next to the slider. Clicking on one of these "bonds" expands the display of the structure in the direction of the bond.

PACK_RADIUS

Move the slider to the right to show all symmetry-equivalent fragments around the current structure within the specified radius. It is also possible to type a number into the box adjacent to the slider.

PACK_LIMITS

This packs one or more unit cells to the limits specified, including fractional limits.
Pack to limits
Displays all fragments of the structure within the limits defined for unit cell edges a, b and c. The numbers in the box are multiples of the edge lengths.
Fill Unit Cell
Displays only those atoms lying within the unit cell.
Complete Fragments
Completes any fragments that are only partially displayed as a result of the various packing options. This is often useful after the Fill Unit Cell command.

HISTORY-TARGET

All refinements and solution of the structure are available from here.

HISTORY

Every step along the process of structure solution and refinement (i.e., every click of the Refine button) is automatically recorded by Olex2 in a "History" database. Each coloured vertical bar in this graph represents a single step along the refinement process. The height of each vertical bar represents the R1 value at that step in the refinement process. Clicking on any of the vertical bars reverts the structure back to its status at that previous step in the refinement. Re-refining at this point creates a new branch in the refinement history (see History Tree below).
Left Arrow
Click on the left arrow to see steps further back in the refinement process.
Right Arrow
Click on the right arrow to see more-recent steps in the refinement process.
Show All Bars
Click this link to show all the steps in the refinement process.
Split Display
Click this link to show only the last few steps in the refinement process.
Scale
Larger numbers of Scale increase the height of the vertical bars, making it easier to distinguish small changes in R1 value between steps in the refinement.
Reload INS
Clicking this link will reload the original .ins file from the current working folder for the structure.
Revert HKL when reverting history
If this box is ticked, when a previous step in the refinement (i.e., vertical bar) is selected from the bar graph above, the .hkl file used will be reverted to the previous version corresponding to that previous step.

HISTORY_TREE

Every time a structure is solved, a new history branch is created. Using the drop-down menu, the latest structure stored in the selected branch will automatically be loaded. It is possible to delete and rename branches. Click on the appropriate structure solution or refinement branch to return to an earlier structure solution or to an entirely different branch of the refinement process.
Condensed
When this box is ticked, an abbreviated version of the history tree will be displayed. If it is left unticked, refinement details for each step will be displayed in the tree.
Popout
Click this link to open a large pop-up window containing the history tree.

NAMING-HELP

NAMING

This tool tab is for naming atoms in a model structure. In some cases, however, it might be more convenient to use the command line to name atoms more efficiently.
Using the Naming Tools
Clicking the Name button enters the naming mode. Once in this mode, the first atom clicked will be named with its element symbol according to the settings specified on this line, and any subsequently clicked atoms will be named in numerical sequence after the first. Press 'ESC' to exit the mode, and 'CTRL+Z' to undo the naming.

Note: When in this mode, the mouse pointer changes to indicate the type of label that would be attached to the next atom clicked.

Start:  The first atom clicked will be named with its element symbol and the number in this box (usually 1).

Suffix:  Appends an optional suffix (e.g., A, _, ') to the atom name.

Type:  If an element is specified in this box, any atom clicked will be converted to this element, and all other name settings on this line will be applied. If no element is specified here, any atom clicked will be named using its own element symbol.
Using the Command Line
$+ html.Snippet(GetVar(default_link),"value=name sel type","hint=name sel type","onclick=name sel type","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will change all currently selected atoms into the element specified by type, e.g., 'name sel N' will convert currently selected atoms to nitrogen.
$+ html.Snippet(GetVar(default_link),"value=name sel integer","hint=name sel integer","onclick=name sel integer","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will renumber all currently selected atoms according to the order in which they were selected, starting from integer, e.g., selecting four carbon atoms and typing 'name sel 3' will name them C3, C4, C5, and C6 in the order of selection.


'CTRL+Z' undoes these changes.

AUTOMATIC_HYDROGEN_NAMING

Olex2 automatically names all hydrogen atoms in a systematic way. This feature can be switched off by unticking the 'Automatic Hydrogen Naming' box if any hydrogens are to have special names.

MATCH_NAMING

If the structure contains two or more equivalent fragments, it is only necessary to name one of them, as Olex2 is capable of applying the same naming scheme to the others. This is helpful when naming atoms in structures with Z' > 1 and also in structures containing a metal center coordinated to more than one ligand of the same type. In the latter case it is necessary to set the maximum number of bonds for the metal to 0 before naming the equivalent fragments. This is done by right-clicking the metal, then setting Bonds to 0 in the menu that appears.

Name all the atoms in the first moiety. Enter a suffix in the Suffix box; this will be appended to atom names in a second identical moiety. Click any one atom of the first moiety, then the corresponding atom in the other moiety (or moieties). Click the Equivalent Fragments (Z' > 1) link to name all the atoms in the second moiety with the same naming scheme as the first, but with the suffix appended. If the Invert for matching box is ticked, the second moiety will be inverted before the naming scheme is applied. This process of copying the naming scheme of the first moiety can then be repeated with each of the other identical moieties in the structure. Reset the number of bonds to the metal center, if necessary.

A few line commands useful for naming are described below. Some of these commands have no equivalent in the GUI.
Add a Suffix
$+ html.Snippet(GetVar(default_link),"value=match sel -n=suffix","hint=match sel -n=suffix","onclick=match sel -n=suffix","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Match naming can also be carried out from the command line. First select two corresponding atoms of two identical moieties. Typing this command will apply the naming scheme used for the first moiety to the second moiety; atom names in the second moiety will have the suffix character appended. For example, 'match sel -n=A' will add the suffix 'A' to the names of the second moiety.

Replace a Suffix
$+ html.Snippet(GetVar(default_link),"value=suffix'>match sel -n=\$suffix","hint=suffix'>match sel -n=\$suffix","onclick=suffix'>match sel -n=\$suffix","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This is similar to Add a Suffix. However, instead of adding a suffix, this command replaces the first character of the original naming scheme with another character. This is useful, for example, if carbons in one ligand are named C101, C102, C103 ... and corresponding atoms in the other ligand are to be named C201, C202, C203 ...

Replace last character
$+ html.Snippet(GetVar(default_link),"value=suffix'>match sel -n=-suffix","hint=suffix'>match sel -n=-suffix","onclick=suffix'>match sel -n=-suffix","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")As in Replace a Suffix, but the last character of the atom name is replaced instead.

REFINE-TARGET

Refine the structure with, e.g., - CTRL+R - >>'refine' - >>'refine 4 4'

REFINE-SETTINGS-TARGET

Open the refinement settings

DRAW-TARGET

Make an image of the structure using the current settings

DRAW-SETTINGS-TARGET

Open the drawing settings

REPORT-TARGET

Generate a report

REPORT-SETTINGS-TARGET

Open the report settings

REFINEMENT_PROGRAM

Apart from its own refinement engine (olex2.refine), Olex2 also supports all variants of ShelXL. Depending on the refinement package, different refinement methods are available.
olex2.refine
The refinement engine built into Olex2. It supports all ShelXL instructions, plus a number of new restraints and constraints that are not available from ShelXL. One can switch between this engine and ShelXL, and Olex2 will not 'forget' the special instructions that are available only in olex2.refine, but of course ShelXL won't heed them.
Methods for olex2.refine
The Gauss-Newton (GN) algorithm  is normally used with olex2.refine. Use the more strongly damped Levenberg-Marquardt (LM) algorithm when the refinement converges poorly.
ShelXL-20XX
Since 2012, updated versions of ShelXL have been released periodically by George Sheldrick. Please check the SHELX website regularly to ensure that the latest versions of the SHELX programs are installed - these are the only versions that should be used. Older versions will still work, however, as long as they are "on the PATH" and are called "shelxl". See Ilia Guzei's manual under the Olex2 Home tab for instructions on how to add a folder to the PATH. Our recommendation is to make a folder called 'CrystallographyPrograms' on the root of a drive and then add that folder to the PATH. Any known executable in that folder will then be available for use within Olex2.
Methods for ShelXL
LS stands for full matrix Least Squares refinement (most suited for small molecule structures). CGLS refers to conjugate gradient least squares refinement (faster than LS when the number of parameters is large, and therefore most suited for early stages of macromolecular structure refinement).
Cycles
This sets the maximum number of refinement cycles for olex2.refine; if the refinement converges earlier, the refinement process will stop automatically. For other refinement programs such as ShelXL, this is the actual number of refinement cycles that will be carried out, regardless of convergence.
Peaks
This specifies the number of residual electron density peaks (Q peaks) to display after refinement.
From the Command Line
$+ html.Snippet(GetVar(default_link),"value=refine 12 5","hint=refine 12 5","onclick=refine 12 5","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This line command will carry out 12 cycles of refinement, after which five residual electron density peaks will be displayed. This number of cycles and peaks will persist in future refinements until changed.

SET_REFLECTION_FILE

The reflection file is specified here; it contains in a condensed form all the data that were collected during the X-ray diffraction experiment.
hkl file
The standard format for a data file containing observed reflections and their intensities from the diffraction experiment is the .hkl file. Select from this drop-down menu the file against which to refine the model. There is no need to rename anything - just choose the file and click Refine.
Other File Formats
Olex2 can also handle file formats such as .raw and others.

WEIGHTS,_EXTINCTION_AND_ACTA


Weight
$+ html.Snippet(GetVar(default_link),"value=weight","hint=weight","onclick=weight","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")A weighting scheme should be applied to the diffraction data once the model is nearly finished and all atoms have settled into their respective positions.
All refinement programs will suggest a suitable weighting scheme. Clicking on the coloured numbers on this line applies the suggested weighting scheme to the data. By ticking the Weight box, Olex2 will automatically update the weights to the suggested values after each refinement cycle. (In practice, this reduces to simply ticking the Weight box after the model has settled and running additional cycles of refinement until the numbers in the Weight boxes turn green.)
Extinction Correction
Extinction is a physical phenomenon affecting the intensity of reflections and can result in certain reflections being systematically absent under certain conditions during the diffraction experiment. The EXTI parameter is designed to account for the intensity changes associated with extinction. The method used is a compromise to account for both primary and secondary extinction. In general, this correction should not be included in refinement until all of the non-hydrogen atoms have been located. Depending on the structural problem, either the EXTI or the SWAT box (see below) can be ticked, but not both. (In practice, first click on the percent sign next to R1 at top to display the Fobs vs Fcalc graph, and if it shows visible downward curvature at high Fcalc, tick the EXTI tickbox and run additional cycles of refinement until convergence is reached.)
SWAT
This is a method for dealing with diffuse solvent regions (usually water in macromolecular structures), by introducing two refinable parameters, g and U. Either EXTI or SWAT can be used, depending on the nature of the structural problem, but not both at once.
ACTA
From the drop-down menu, select No ACTA to omit writing a CIF file, ACTA NOHKL to write a CIF file without an embedded hkl file, and ACTA to write a CIF file with an embedded hkl file. It is recommended always to use the ACTA option.

REFINEMENT_MASKS

In some structures, solvent disorder can be so severe that modelling this disorder using atomic sites (i.e., discrete, partially occupied atoms) is neither possible nor sensible. In these cases, it is better not to even attempt to model the disordered region, but simply to leave the measured electron density in place. This solvent masking technique requires the calculation of the area to be excluded from the refinement - and defining that depends on the structure at hand.

Watch the video!

The implementation of solvent masking in Olex2 is based on the BYPASS paper by P. van der Sluis and A. L. Spek.
Use solvent mask
Ticking this box includes in the refinement a solvent contribution to the structure factors as the discrete Fourier transform of the electron density in the solvent area. The solvent mask is a region occupied by disordered solvent. It can be calculated and displayed under Tools > Maps > Masks (select wire in the drop-down menu under View in the Maps tool tab). With olex2.refine, the solvent contribution is added internally to that calculated from the ordered part, whereas with ShelXL the solvent contribution is subtracted from the observed data and a modified hkl file is passed to the external refinement program.
Update mask
When ticked, the solvent mask will be recomputed before the start of the refinement. This can lead to an improved solvent mask, particularly if the ordered part of the structure was poorly converged before the initial mask search.
Solvent r
Only grid points within cavities larger than a certain solvent radius (r) are taken into account in the calculation. The default value is 1.2 Å, which prevents displaying voids in which no atom could fit.
Truncation
This value is used to define a more close-fitting solvent mask than would be possible with the solvent radius r alone. It is usually very close, if not equal, to the solvent radius r.

MASKING_INFO

This is where information about the contents of the masked region is displayed. For each solvent void, the table displays its volume in Å3 and the number of electrons it contains. When using a solvent mask, it is best practice after refinement is complete to enter the estimated contents of the void(s) in this table for inclusion in the CIF file. This is done by clicking the Edit button under Content/Asymmetric Unit in the table and typing in the number and name of the solvent molecules present in the void(s), e.g., '1/2 toluene' or 'CH2Cl2'.

Once the void contents have been entered, Olex2 will calculate the number of electrons for the contents and if there is a close match with the number of electrons in the actual contents, both e- numbers will turn green. A panel will appear containing the Formula and Moiety chemical formulas, as well as another Edit button for editing any information that is to be included in the CIF file. Sample explanatory text for the solvent masking process for the structure is provided in the Use & Edit panel. This text should be edited as necessary and included in the edit_mask_special_details section of the CIF file.

REFINEMENT_SETTINGS_EXTRA

Some refinement programs may have extra settings that are not accessible through the Olex2 GUI; these extra settings may be specified here.

COLLECTION-TARGET

Sample ID and submitter information

CRYSTAL-TARGET

Compound name; crystal size, shape, color, etc.

CRYSTAL_IMAGE-TARGET

Pictures of the crystal

DIFFRACTION-TARGET

Diffractometer information, temperature, refinement details, etc.

ABSORPTION_CORRECTION-TARGET

Absorption correction details

PUBLICATION-TARGET

Publication and author information

CITATIONS-TARGET

Citations for software and modules used in solution and refinement

REFERENCE-TARGET

CSD refcode and journal information

SOURCE_FILES-TARGET

Files from which CIF information is collated

REPORT_SETTINGS_1

This is a collection of tools to create (a) a report about the structure in HTML format, and (b) a CIF file for the structure.

Choose the report name (the default name is the same as the name of the current file open in Olex2) and select from the drop-down menu the image to be included in the report. The drop-down menu shows all image files in the working folder for the structure. Once the other report settings below have been selected, click HTML Report to create a report as a .HTML file in the working folder for the structure.

REPORT_SETTINGS_2

Select a style and the format for the header and footer for the report.

REPORT_SETTINGS_3

Select a style for displaying numbers and suffixes in atom labels in the report.

H3-COLLECTION-HELP

COLLECTION

Enter data collection information here, including Sample ID; Submitter and Operator names; and various dates.

Information entered in these boxes will take precedence over information provided in other files when the CIF file is written. If the CIF information is edited using the Edit CIF Info button below, then that will take precedence over what is entered here, and those new values will be displayed in these boxes.

H3-CRYSTAL-HELP

CRYSTAL

Enter information here pertaining to the actual crystal used for the diffraction experiment: the Systematic Name of the compound, if known (enter '?' if unknown); Colour (usually extracted automatically from .CIF_OD file); Size (dimensions in mm) and Shape (crystal description chosen from drop-down menu); synthesis method used to make the compound (Preparation Details); Crystallisation Details (technique used for growing the crystal); and Crystal Mounting technique.

Information entered in these boxes will take precedence over information provided in other files when the CIF file is written. If the CIF information is edited using the Edit CIF Info button below, then that will take precedence over what is entered here, and those new values will be displayed in these boxes.

CRYSTAL_IMAGE

Any photographs taken of the crystal present in the 'movie' folder in the working folder for the structure will be viewable here. A series of photographs (e.g., of the mounted crystal rotating on the goniometer) can be played as an animation by pressing the Play button in this panel.

H3-DIFFRACTION-HELP

DIFFRACTION

Enter information about the diffraction experiment here: Diffractometer type; other diffractometer/diffraction details (click the Definition File link to select a diffractometer from the window that opens); and Diffraction and Cell Measurement temperatures. Other Special Details of the experiment and of the refinement (e.g., disorder treatment, solvent masking) may be typed into the respective boxes provided.

Information entered in these boxes will take precedence over information provided in other files when the CIF file is written. If the CIF information is edited using the Edit CIF Info button below, then that will take precedence over what is entered here, and those new values will be displayed in these boxes.

H3-ABSORPTION_CORRECTION-HELP

ABSORPTION_CORRECTION

Information about the type of absorption correction employed in the experiment (Type; Details of the correction method; absorption Tmax and Tmin) will be automatically extracted from files created during the experiment and entered into these boxes. If any information is missing, it can be entered manually here.

H3-PUBLICATION-HELP

PUBLICATION

Enter the following details related to publications here, to be included in the CIF file: CCDC number for the structure (if known); Contact author and any additional authors on the article (added from the user database); Journal name; and Journal style (general or Acta Cryst.). Click the Contact Letter link to type an entry for the _publ_contact_letter field of the CIF.

Information entered in these boxes will take precedence over information provided in other files when the CIF file is written. If the CIF information is edited using the Edit CIF Info button below, then that will take precedence over what is entered here, and those new values will be displayed in these boxes.

CITATIONS

Olex2 automatically creates literature citations for all software, including plugins, used during structure determination (if invoked through Olex2 or found in the source files).

REFERENCE

Further details about the journal in which the structure is published may be entered here: the CSD Refcode for the structure (if known); list of Authors on the article; Journal name; Volume number of journal; article Page numbers; and publication Year. A Comment on the publication may be entered in the final box in this panel.

Information entered in these boxes will take precedence over information provided in other files when the CIF file is written. If the CIF information is edited using the Edit CIF Info button below, then that will take precedence over what is entered here, and those new values will be displayed in these boxes.

H3-SOURCE_FILES-HELP

SOURCE_FILES

This tool tab lists the source files used by Olex2 to construct a CIF file for the structure and prints a warning if there is conflicting information among the sources.

METADATA_SOURCES

Olex2 searches the working folder for sources of metadata such as diffractometer information and data collection parameters, for incorporation into the final CIF file created for the structure after refinement is complete. Such details are normally recorded during the diffraction experiment in a .CIF_OD file. If no files containing metadata are found, Olex2 prints out a brief message to that effect.

METADATA_CONFLICTS

Olex2 automatically extracts relevant information from metadata source files for inclusion in the final CIF, but the process is not always straightforward because the sources may contain conflicting information. In this case, Olex2 prints an error message and the user has to resolve the conflicts manually, i.e., choose the correct information source for the CIF data.

To remove the There are unresolved conflicts error message, collapse the Report tab and re-expand it, then resolve the conflicts in the window that opens. Click on the Source Files tool tab to open and close it. Olex2 will now display a message confirming that all conflicts have been resolved. The Show ALL link lists all the sources of CIF data and the Reset Previously Resolved Conflicts link removes any manually entered information (causing any previous conflicts to reoccur).

CIF-PART-1-HELP

CIF_PART_1

This section deals with the creation and modification of the CIF file, which contains everything known about the structure in a format defined by the IUCr. A complete and correct CIF file is vital for the successful publication of a structure in any peer-reviewed journal. Creation of the CIF is normally handled automatically by Olex2, but these tools are provided in case the CIF needs to be modified.
Edit CIF Info
Pressing this button will open a file containing all the information that Olex2 will add to the CIF file when it is created. Information entered in the above tool tabs (Collection, Crystal, Diffraction, etc.) will appear here. It is possible to modify the contents of this file, and even add or remove entries. Edits made here will take precedence over any other previously entered values, and the values entered using Edit CIF Info will appear when the above tool tabs are reopened.
Merge CIF
Clicking Merge CIF will take the metadata from the source files, the tool tabs above, and information entered using the Edit CIF Info button, and merge them into the CIF created during the last cycle of refinement. This final CIF will then be opened in the default text editor.
Include/Exclude HKL and RES in your CIF
Select from the drop-down menu how reflection data and refinement instructions will be included in the final CIF. Leave as is includes the .hkl and .res files as returned by the refinement program. ShelXL includes the HKL and RES information as plain text by default. Include incorporates the HKL/RES information in the CIF as a loop (IUCr format). Exclude leaves out both the HKL and RES information - this option is strongly discouraged.

CIF-PART-2-HELP

CIF_PART_2

The IUCr offer a free error-checking service called checkCIF  for validating CIF files.
IUCr checkCIF Report
Click the IUCr checkCIF button to send the merged CIF to this service for checking. The resulting checkCIF  report may be received in PDF or in HTML format (select from drop-down menu). The report helps identify potential problems with the structure. For full validation of both the CIF and the structure factors, it will also be necessary to upload the structure factors as a .fcf file. For this and other checkCIF  options, see the checkCIF website.
Depositing a structure with the CCDC
There are two types of submissions to the Cambridge Crystallographic Data Centre (CCDC).

Request CCDC Number:  Submitting a structure to the Cambridge Structural Database  (CSD) is now a requirement for most journals. Click this button to send the CIF file and the optional structure factor file to the CCDC. Once the CIF has been processed, a unique CCDC number will be assigned to the structure and sent by email to the depositing author, usually within a few days. This is the number that needs to be provided to the journal in which the structure is to be published.

Note: To expedite processing, it is important that all the required data are provided, i.e., the CCDC forms need to be filled out as completely as possible.

If any structure is not published within three years and no other instructions have been received, the CCDC will attempt to contact the depositing author and the corresponding author by e-mail. If no response is obtained, the CCDC will retain the data indefinitely pending future publication.

Publish as CSD Communication:  Sometimes, a structure is not intended for publication in a scientific journal, but is deposited with the CSD to make it available to other scientists. In such cases, it is possible to publish the structure as a "CSD Communication" by authorising the CCDC to include it directly in the CSD, which occurs as soon as the structure is processed by the CCDC.

Please refer to this blog and these instructions for more details about CSD Communications.

CIF-PART-3-HELP

CIF_PART_3

One of the really strong points of Olex2 is that it will keep CIF information synchronised throughout the entire solution and refinement process. This is quite a tricky thing to do, but if it all works the way it should, it will never be necessary to edit a CIF by hand again.
Merge CIF 1
This tick-box is included here only for the very rare cases when problems occur in merging CIF data from the refinement program and information obtained by Olex2. If this box is ticked, as is normally the case, the files that are listed on this line will all be merged with the CIF information. If anything goes dreadfully wrong here with the construction of the final CIF file, untick this box. However, this is really not recommended, and if it ever necessary to untick the box, please send an email describing the problem to support@olex2.org so that the issue can be fixed.
metacif
The metacif link opens the file in which Olex2 collects all the information available about the structure. It is also possible to open this file using the Edit CIF Info button above, and any edits made will take precedence over all other sources of information, as mentioned earlier.
Add local/default CIF
This features allows information from an external CIF file to be added to the CIF file being constructed for the current structure. Click local if the external CIF file is in the current working folder or default to access any of the built-in CIF files of Olex2, e.g., to add information for a specific diffractometer.

CIF_PART_4

Tick this box to force information from metacif to be merged into the final CIF for the structure. Normally, items such as refinement details (and other items listed in the "skip_merge" section of the Olex2 system file customisation.xlt) are obtained from the refinement program, not from metacif, so this box is usually left unticked.

ABS_STR

The value of the Flack parameter x and Hooft parameter y are given here for chiral structures. For a correctly determined absolute structure, both are close to 0. If they are close to 1, it may be necessary to invert the structure with 'inv -f'. Select from the drop-down menu the method used to determine the absolute structure (most commonly Anomalous dispersion).

SELECT-ATOMS-HELP

SELECT_ATOMS

This menu provides several methods of selecting or deselecting atoms with varying degrees of specificity. Press 'ESC' at any time to deselect everything.
Exclusive
Selects only atoms of the element clicked.
Additive
Adds all atoms of the element clicked to the selection.
Command Line Examples
$+ html.Snippet(GetVar(default_link),"value=sel \$c","hint=sel \$c","onclick=sel \$c","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Selects all C atoms.
$+ html.Snippet(GetVar(default_link),"value=sel -u","hint=sel -u","onclick=sel -u","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Deselects (unselects) everything.
$+ html.Snippet(GetVar(default_link),"value=sel c1","hint=sel c1","onclick=sel c1","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Selects atom C1.
$+ html.Snippet(GetVar(default_link),"value=sel \$c \$n","hint=sel \$c \$n","onclick=sel \$c \$n","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Selects all C and N atoms.

SELECTIONS

Once atoms and/or bonds are selected, the following links can be clicked to perform specific actions:
Invert
$+ html.Snippet(GetVar(default_link),"value=sel -i","hint=sel -i","onclick=sel -i","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Inverts the current selection, i.e., all atoms and bonds not not currently selected will be selected instead.

Deselect
$+ html.Snippet(GetVar(default_link),"value=sel -u","hint=sel -u","onclick=sel -u","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Deselects (unselects) all selected atoms.

Delete
$+ html.Snippet(GetVar(default_link),"value=kill sel","hint=kill sel","onclick=kill sel","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Deletes all selected atoms; the same as pressing the 'Delete' key. Undo the deletion with 'CTRL+Z'.

Previous Selection
$+ html.Snippet(GetVar(default_link),"value=selback","hint=selback","onclick=selback","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Re-select all atoms previously selected.

SELECT-CRITERIA-HELP

SELECT_CRITERIA

To select atoms on the basis of their Uiso values, choose the >, <, or = operator from the drop-down menu and enter a Uiso value in the box. Then click Select to select only those atoms meeting the specified criterion.

SELECT-RINGS-HELP

SELECT_RINGS

Select all rings of the specified type, e.g., C6, C5N, C5, or C5O, within the structure. It is possible to specify other rings by typing them directly into the drop-down menu, e.g., C3N2 will find all five-membered rings consisting of three carbons and two nitrogens (imidazoles and pyrazoles). Click outside the menu to highlight the specified ring. (The Phenyl and Pyridine links are provided for convenience.)

SOLVE-TARGET

Solve the structure

SOLVE-SETTINGS-TARGET

Open the solution settings

SOLUTION_PROGRAM

If particular solution programs are installed in a standard way on the system, Olex2 will find them and they will appear automatically as a choice in the Program drop-down menu. If they don't appear, please make sure that the directory where they are installed is either on the System Path, or has been entered under Home > Settings > Path. Ilia Guzei's manual, linked in the Start tool tab under the Home tab, gives detailed instructions for the installation of solution programs.
Choice of Programs
Olex2 can make use of many structure solution programs such as:
  • ShelXT
  • ShelXS
  • ShelXD
  • olex2.solve
  • SuperFlip
  • Sir2011
  • Sir2008

Solution Method
Select the method to use for the selected structure solution program. This is only really relevant for ShelXS - all other programs only have one solution method!

CHEMICAL_FORMULA

The expected chemical composition for the structure. The presence of heavy atoms in the expected composition when they are not actually present in the structure can adversely affect some structure solution programs. Likewise, omitting a heavy atom from the expected composition when one is actually present in the structure can also cause problems in structure solution.
Z
Z denotes the number of formula units in the unit cell. For molecular compounds Z is the number of full molecules in the unit cell. For continuous solids and structures that need to be "grown" (see View > Symmetry Generation > Growing) it is less easy to determine Z, but it is generally the number of formula units in the unit cell.
Z'
The closely related parameter Z' (Z prime) denotes the number of formula units in the asymmetric unit.

SPACE-GROUP-HELP

SPACE_GROUP

The space group is usually determined during data acquisition and processing.
Suggest SG
$+ html.Snippet(GetVar(default_link),"value=sg","hint=sg","onclick=sg","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Olex2 can also determine the space group. Click Suggest SG and the most likely choices will appear in the drop-down menu on the right. Type 'text', if necessary, to open a text file containing the full output of the space group likelihood analysis. Select a space group from the drop-down menu before proceeding to refinement.


It is also possible to type a space group directly into the menu box on this line. Click anywhere outside the box to ready the structure for solution in the specified space group.

SOLUTION_SETTINGS_EXTRA

Some solution programs may have associated extra settings not available through the GUI; these extra settings may be specified here.

CF

There are several variables whose settings can influence the Charge Flipping solution:

AMPT - Charge flipping can be done on F, E, or quasi-E.

MAPT - Maximum number of attempts to find a Phase Transition

MACM - Maximum number of attempts to get a sharp Correlation Map

MASI - Maximum number of Solving Iterations

SORT_ORDER

Sort atoms in the structure according to the categories shown in the drop-down menus. Atoms are sorted starting with the left-most category, then by further sub-categories proceeding to the right. For example, suppose the first category is Part, the second Z, the third Label, and the fourth Suffix. When the Sort button is clicked, the atoms will be sorted according to increasing PART number first, then according to decreasing atomic number Z, then according to increasing label number, and finally according to increasing suffix.

Note: Any hydrogen atoms attached to other atoms will be sorted along with the atoms to which they are attached.

MOIETY

If None is selected in the Moiety drop-down menu, all atoms in the structure will be sorted regardless of which fragment they are in, according to the categories chosen in Sort Order. If a category is chosen here, all fragments composing the structure will first be sorted based on the chosen category, after which atoms will be sorted within each moiety according to the Sort Order categories. For example, suppose a structure has two fragments, one large and one small, and Size is selected from the moiety drop-down menu. When the Sort button is clicked, the atoms in the large fragment will be listed first in sort order, followed by the atoms in the small fragment, also in sort order.

SPECIFIC_ORDER

When the Sort button is clicked, atoms in the structure will be sorted according to the order specified in these boxes.

TOOLBOX_WORK-TARGET

A collection of useful tools - Make all peaks Carbon - Move Atoms - Show/Hide Peaks - Expand Short Contacts - Peak Slider - Disorder Tools

CHANGE_ELEMENT-TARGET

Change atom types to 

ANIS-TARGET

Make selected atoms anisotropic. If no atoms are selected, all atoms will be transformed.

ISOT-TARGET

Make selected atoms isotropic. If no atoms are selected, all atoms will be transformed.

QC-TARGET

Convert all Q peaks to C

QH-TARGET

Convert all Q peaks to H

TIDY-TARGET

Tidy up your structure. Only recommended in early stages of refinement!

KILLH-TARGET

Deletes all H atoms from the model. Undo with CTRL+Z.

Q-TARGET

Toggle among three states: show Q peaks, show Q peaks with bonds, or hide Q peaks

H-TARGET

Toggle among three states: show hydrogens, show hydrogens with H-bonds, or hide hydrogens

CENTER-TARGET

Center the structure on the screen and adjust the zoom level

OK-TARGET

Adjust the chemical formula to what is present in the model. The value of Z' will be taken into account, so check it!

DISORDER_TOOLS-TARGET

Tools for dealing with disordered structures

PEAK_&_UISO_SLIDERS-TARGET

Sliding scales for Q peak and atom selection

GROWING-TARGET

Expand the structure on the screen

FINISHING-TARGET

Tools for quickly sorting atoms and making images

LABELS

It is possible to customise the labels in the model display. If a particular property is not applicable to any atom, there will be no label, e.g., if 'labels -o' (see below) is typed and all atoms have occupancy 1, no atoms will be labelled.
$+ html.Snippet(GetVar(default_link),"value=help labels","hint=help labels","onclick=help labels","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Print all options for the 'labels' command.


Atom Names:  
$+ html.Snippet(GetVar(default_link),"value=labels -l","hint=labels -l","onclick=labels -l","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")All atom names of non-hydrogen atoms will be displayed next to the atoms.


Crystallographic Occupancy:  
$+ html.Snippet(GetVar(default_link),"value=labels -o","hint=labels -o","onclick=labels -o","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This displays the crystallographic occupancy of any atoms which are not 100% occupied, i.e., whose occupancy is not 1.


Chemical Occupancy:  
$+ html.Snippet(GetVar(default_link),"value=labels -co","hint=labels -co","onclick=labels -co","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Labels atoms with their "chemical occupancy" if less than 1. Basically the same as Crystallographic Occupancy above, but the occupancy values for atoms located on symmetry elements are not shown.


Parts:  
$+ html.Snippet(GetVar(default_link),"value=labels -p","hint=labels -p","onclick=labels -p","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Displays PART numbers for any atoms not in PART 0.


Link-Code:  
$+ html.Snippet(GetVar(default_link),"value=labels -lo","hint=labels -lo","onclick=labels -lo","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")If there are atoms in the structure whose occupancies are linked, their link codes will be shown (FVAR 21/-21 in ShelXL language).


Fixed Parameters:  
$+ html.Snippet(GetVar(default_link),"value=labels -f","hint=labels -f","onclick=labels -f","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Labels all atoms with fixed occupancy, regardless of the actual value of the occupancy.


Variables:  
$+ html.Snippet(GetVar(default_link),"value=labels -v","hint=labels -v","onclick=labels -v","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Displays any atoms whose occupancy is linked to any variable.


AFIX Commands:  
$+ html.Snippet(GetVar(default_link),"value=labels -a -h","hint=labels -a -h","onclick=labels -a -h","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This is useful to check the AFIX commands that are being applied to the structure.


Q-Peak Intensities:  
$+ html.Snippet(GetVar(default_link),"value=labels -qi","hint=labels -qi","onclick=labels -qi","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Relative intensities of Q peaks will be displayed on the structure.


Ueq:  
$+ html.Snippet(GetVar(default_link),"value=labels -u","hint=labels -u","onclick=labels -u","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Labels atoms with their Ueq values.


Label + residue rumber:  
$+ html.Snippet(GetVar(default_link),"value=labels -l -rn","hint=labels -l -rn","onclick=labels -l -rn","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Displays both atom label and residue number.


Residue numbers:  
$+ html.Snippet(GetVar(default_link),"value=labels -rn","hint=labels -rn","onclick=labels -rn","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows the residue number to which an atom belongs.


Residue class:  
$+ html.Snippet(GetVar(default_link),"value=labels -rc","hint=labels -rc","onclick=labels -rc","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows the residue class to which an atom belongs.

Label H
Ticking this box will display labels on hydrogen atoms (unlabeled by default) after a selection is made from the Labels drop-down menu.

H Atom Labels:  
$+ html.Snippet(GetVar(default_link),"value=labels -h -l","hint=labels -h -l","onclick=labels -h -l","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This will label all atoms, including hydrogen atoms, and Q peaks with their atom name labels.

Hide
Press this button to hide atom or Q-peak labels. It will switch other types of labelling (e.g., occupancy, AFIX codes) off as well. Pressing 'F3' toggles the display of atom and Q-peak labels on and off.

TOOLBAR_MODEL

This is a collection of three basic tools needed for model building.
Assign Atom Types
Each element currently in the formula is represented by a small button.

Using the GUI:  
$spy.MakeElementButtonsFromFormula('mode')All atoms present in the model are shown. The '...' button opens the Periodic Table if more elements need to be added.
Clicking on an element button launches the atom type assignment mode for this particular element. In this mode, any atoms or Q peaks clicked are converted to that element. Pressing the 'ESC' key exits the mode. Alternatively, selecting atoms first and then clicking an element button turns them all into that element. The buttons on this row will be red or blue if there is a mismatch between the number of atoms of that element in your model and those in the chemical formula. They turn green if the numbers agree.

Using the Command Line:  It is usually much more efficient to assign elements using the keyboard. Here are three frequently used commands:
$+ html.Snippet(GetVar(default_link),"value=name sel C","hint=name sel C","onclick=name sel C","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Turns all selected atoms to carbons.
$+ html.Snippet(GetVar(default_link),"value=mode name C","hint=mode name C","onclick=mode name C","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Enter atom naming mode; once in the mode, all atoms clicked will turn to carbons.
$+ html.Snippet(GetVar(default_link),"value=name \$Q C","hint=name \$Q C","onclick=name \$Q C","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Turns all Q peaks to carbons.


Note: If the box on this line is ticked, then a cycle of refinement will immediately be carried out when any of the following buttons is clicked:
Add H - Geometrically Place Hydrogen Atoms
Clicking this button will cause Olex2 to place hydrogen atoms geometrically on any selected atom(s). If no atoms are selected, hydrogens will be placed on all possible atoms, to complete the structure.
$+ html.Snippet(GetVar(default_link),"value=hadd","hint=hadd","onclick=hadd","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Adds hydrogen atoms to selected atoms (or to all atoms, if none are selected).
$+ html.Snippet(GetVar(default_link),"value=hadd 137","hint=hadd 137","onclick=hadd 137","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Will use specifed AFIX if possible. (137 adds three hydrogen atoms to a methyl group, for example.)
$+ html.Snippet(GetVar(default_link),"value=hadd -137","hint=hadd -137","onclick=hadd -137","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")If the connectivity does not allow the addition of the specified AFIX atoms, it is still possible to place them in this way. First select the atom to which hydrogen atoms are to be added, then select a second atom to define a vector.

Make Atoms Anisotropic
Clicking the ellipsoid button makes the selected atoms anisotropic. If no atoms are selected, this change will be applied to all atoms.
$+ html.Snippet(GetVar(default_link),"value=anis","hint=anis","onclick=anis","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")All selected atoms will be refined anisotropically (ellipsoids will result).

Make Atoms Isotropic
Clicking the sphere button makes the selected atoms isotropic. If no atoms are selected, this change will be applied to all atoms.
$+ html.Snippet(GetVar(default_link),"value=isot","hint=isot","onclick=isot","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")All selected atoms will be refined isotropically (spheres will result).

QUICKTOOLS

This is a further selection of tools useful for model building.
Change type and display of atoms
$+ html.Snippet(GetVar(default_link),"value=name \$Q C","hint=name \$Q C","onclick=name \$Q C","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")$spy.MakeHoverButton('toolbar-QC','name \$Q C')This tool will change all displayed electron density peaks (Q peaks) to carbon atoms, regardless of peak height.
$+ html.Snippet(GetVar(default_link),"value=name \$Q H","hint=name \$Q H","onclick=name \$Q H","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")$spy.MakeHoverButton('toolbar-QH','name \$Q H')All visible Q peaks will be changed to hydrogens.
$+ html.Snippet(GetVar(default_link),"value=clean","hint=clean","onclick=clean","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")$spy.MakeHoverButton('toolbar-tidy','clean')Tidy the structure: small and geometrically impossible peaks will be removed; all remaining peaks will be changed to carbons.
$+ html.Snippet(GetVar(default_link),"value=kill \$H","hint=kill \$H","onclick=kill \$H","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")$spy.MakeHoverButton('toolbar-killH','kill \$H')Deletes all selected hydrogen atoms from the structure. If no hydrogen atoms are selected, all will be deleted. Undo with 'CTRL+Z'.
$+ html.Snippet(GetVar(default_link),"value=showQ","hint=showQ","onclick=showQ","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")$spy.MakeHoverButton('toolbar-Q','showQ')'CTRL+Q'. Toggle among three states: show electron density peaks, show them with bonds to nearby atoms, or hide them.
$+ html.Snippet(GetVar(default_link),"value=showH","hint=showH","onclick=showH","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")$spy.MakeHoverButton('toolbar-H','showH')'CTRL+H'. Toggle among three states: show H atoms, show them with H-bonds, or hide them. Hydrogen atoms remain in the model, regardless of their display.
$+ html.Snippet(GetVar(default_link),"value=compaq>>compaq-a>>center","hint=compaq>>compaq-a>>center","onclick=compaq>>compaq-a>>center","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")$spy.MakeHoverButton('toolbar-center','compaq>>compaq -a>>center')Fragments will be assembled and the structure will be centered on the screen.

Specifying the formula of the structure
Z'=Set the value of Z' here. (Z' is the number of formula units in the asymmetric unit.) For a molecular structure, Z' is typically 1. If there are two independent molecules on the screen, Z' must be set to 2. If the molecule sits on a symmetry element and has to be "grown" (i.e., expanded by symmetry operations - see Growing tool tab below) to be displayed in full, Z' will be smaller than 1, often 0.5.
$+ html.Snippet(GetVar(default_link),"value=fixunit","hint=fixunit","onclick=fixunit","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")$spy.MakeHoverButton('toolbar-OK','fixunit')Adjusts the sum formula to include only atoms currently present in the model, taking the value of Z' into account.

ELECTRON_DENSITY_QUICK_MAPS

This tool tab provides options for the calculation of various electron density maps, which can be displayed in different 2D or 3D formats using the tools in this tab. However, when the Level setting (see Maps tool tab help) approaches zero, electron density maps become very messy and slow to display, so Olex2 does not display these regions.
Available maps


diff:  Will display the difference map, Fobs-Fcalc. Make sure to select surface, wire, or points from the View drop-down menu under the Maps tool tab (accessed through Map Settings in this tool tab) for this map to be displayed correctly. The corresponding line command is 'CalcFourier -diff -r=0.1 -m' or simply 'CTRL+M'. This is an extremely important tool for checking the validity of a model. Red regions of the map represent areas of missing electron density and green regions represent areas of excess electron density. Both red and green regions will be very small in an accurate model of the structure.

Fcalc:  Will display the calculated electron density.

2Fo-Fc:  Will display the map of 2Fobs-Fcalc.

Fobs:  Will display the observed electron density map.

Deformation:  Will display a deformation electron density map (deviations from spherical atom model).

PDF:  Will display a probability density function map for evaluating the quality of an anharmonic refinement.
Show Map
Turns the display of the currently selected map on.
Hide Map
Turns the display of the currently selected map off.
Map Settings
This opens the Maps tool tab under Tools for further customising the map display.

DISORDER_TOOLS

These are extremely useful commands for dealing with crystallographic disorder.

PART_LINKS

This is a selection of tools for displaying selected PARTs in the structure. The command-line equivalents are also very useful to know:
$+ html.Snippet(GetVar(default_link),"value=showp 0 1","hint=showp 0 1","onclick=showp 0 1","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows all atoms in no particular PART (equivalently, in PART 0) and all atoms in PART 1.
$+ html.Snippet(GetVar(default_link),"value=showp 0 2","hint=showp 0 2","onclick=showp 0 2","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows all atoms in no particular PART (equivalently, in PART 0) and all atoms in PART 2.
$+ html.Snippet(GetVar(default_link),"value=showp 1","hint=showp 1","onclick=showp 1","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows only the atoms PART 1.
$+ html.Snippet(GetVar(default_link),"value=showp","hint=showp","onclick=showp","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows all atoms in all PARTs.
$+ html.Snippet(GetVar(default_link),"value=sel part 1","hint=sel part 1","onclick=sel part 1","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Selects all atoms in PART 1.


If the Sel box is ticked when 0||1 or 0||2 is clicked, atoms in PART 1 or PART 2, respectively, will be selected in the display. If the Unique box is ticked, a list of unique atoms in the structure will be printed in the display output. Atoms will be marked with the parameter selected in the drop-down menu: Occupancy will indicate the occupancy of any partially occupied sites as a decimal number, Chem Occ. will display the chemical occupancy of each partially occupied site, Link-Code will display the link code for atoms whose occupancies are linked in ShelX format, PART No will show any non-zero PART numbers of atoms, and Labels will display atom labels.

The use of the UP arrow key to repeat recently issued commands is particularly useful here!

FIT_AND_SPLIT_GROUP

The fit and split tools operate on one or more selected atoms. To fit an atom (or group of atoms) is to move it to a desired location in the model. To split an atom (or group of atoms) is to divide it into two parts by creating a duplicate, which can then be moved to a desired location, e.g., to model disorder in the structure.
Fit or Split One Atom
Left-click on an atom to highlight it. To fit the atom, click the Fit button. The color of the atom changes. Now hold down the 'SHIFT' key and drag the atom with the left mouse button to any desired position. Press the 'ESC' key to exit the Fit/Split mode. The fitted atom will remain in its new position.

To split the atom in two, click the Split button. The color of the atom changes as before, but dragging the atom with the 'SHIFT' key pressed moves only ONE of the two atoms that were created by the Split command (the other atom can be moved with a separate Fit command, as above). The occupancies of the two atoms are linked, and the atoms will now have different PART numbers. Press the 'ESC' key to exit the Fit/Split mode; the moved atom will remain in place.
Fit or Split Two Atoms
Select two atoms, then click either the Fit or the Split button. Split will generate a duplicate pair, Fit will not. The color of the atoms changes. Drag the atoms with the mouse while pressing the 'SHIFT' key to move them together as a group to any desired position.

To rotate the atoms about their midpoint instead of moving them, hold down the 'CTRL' key while dragging with the mouse. Press 'ESC' to exit the Fit/Split mode; the moved pair of atoms will remain in place.
Fit or Split Three or more Atoms
Select three or more atoms, then click either the Fit or the Split button. As before, Split will generate a duplicate group, but Fit will not, and the atoms will change color. The entire group can be moved to any desired position by dragging it while holding down the 'SHIFT' key (or rotated if the 'CTRL' key is held down instead).

It is also possible to rotate the group about one of its bonds. First activate the bond about which you wish to rotate the group by right-clicking on it. Now, dragging the group while holding down the 'CTRL' key rotates the group around this activated bond. Press 'ESC' to exit this mode; any moved atoms will remain in their new positions.
Split with SAME
This is one of the most powerful tools in Olex2. If a grouping of atoms is disordered, and one of the parts can be modelled (no matter how badly), the Split button with the SAME restraint will be very useful. (Typing 'mode fit -s same' is equivalent to clicking the Split button with this restraint active.) Note that the SAME restraint is applied by default in Olex2 when splitting a group; other restraints may be selected from the drop-down menu. Everything will be restrained, so if the disorder can be modelled, the refinement process will sort it out automatically, though sometimes a large number of refinement cycles will be needed.
Split with RIGU
As Split with SAME, except that the RIGU "rigid-bond" restraint is applied instead when splitting a group. See the Shelx Compatible Restraints tool tab help for more details on RIGU.
Split with SAME, RIGU
As above, except that both SAME and RIGU restraints are applied when splitting a group.

PEAK_&_UISO_SLIDERS

This tool tab provides tools for selecting Q peaks and atoms according to their properties.

ELECTRON_DENSITY_PEAK_SLIDER

This tool enables the selection of Q peaks by intensity.

Starting from the middle of the scale at 100, move the Peaks slider to the left to filter out the weakest Q peaks first, or to the right to filter out the strongest Q peaks first. Any commands issued after filtering will only apply to the remaining visible peaks. For example, the line command 'name \$Q C' will convert all visible Q peaks to carbons, and clicking Select or Delete will select or delete the peaks, respectively.

UISO_SELECT_SLIDER

This tool allows the selection of atoms according to their Uiso values.
Slide to the RIGHT
Starting from the middle of the scale, move the Uiso slider to the right to select atoms whose Uiso value is larger than the value indicated next to the slider.
$+ html.Snippet(GetVar(default_link),"value=sel atoms where xatom.uiso < 0.02","hint=sel atoms where xatom.uiso < 0.02","onclick=sel atoms where xatom.uiso < 0.02","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Selects all atoms whose Uiso value is less than 0.02.

Slide to the LEFT
Starting from the middle of the scale, move the Uiso slider to the left to select atoms whose Uiso value is SMALLER than the value indicated next to the slider.
$+ html.Snippet(GetVar(default_link),"value=sel atoms where xatom.uiso > 0.04","hint=sel atoms where xatom.uiso > 0.04","onclick=sel atoms where xatom.uiso > 0.04","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Selects all atoms whose Uiso value is greater than 0.04.

GROWING

Olex2 shows the asymmetric unit by default. This tool tab contains very powerful techniques for "assembling" a structure model on the screen exactly as desired. It is then possible to refine the model repeatedly in Olex2 without dismantling this assembly.

GROW


Growing
Growing here is used as a general term for adding atoms to the existing model on the screen in some systematic way, e.g., by adding symmetry-equivalent atoms to visualize an entire molecule when the asymmetric unit shows only part of the molecule because Z' < 1 for the structure.

Grow All:  
$+ html.Snippet(GetVar(default_link),"value=grow","hint=grow","onclick=grow","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Generates all "missing" connected symmetry-equivalent atoms. This will usually suffice to expand an asymmetric unit to show a complete molecule.


Shells:  
$+ html.Snippet(GetVar(default_link),"value=grow -s","hint=grow -s","onclick=grow -s","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This adds atoms in concentric shells outward from the structure currently displayed on the screen.


Complete:  
$+ html.Snippet(GetVar(default_link),"value=grow -w","hint=grow -w","onclick=grow -w","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Generates all missing symmetry-equivalent atoms of an already grown structure, whether bound to the main fragment or not. Thus, this command will display symmetry-equivalent solvent molecules and counter-ions not generated by a plain 'grow' command.


Asymmetric Unit:  
$+ html.Snippet(GetVar(default_link),"value=fuse","hint=fuse","onclick=fuse","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Removes all symmetry-equivalent atoms and displays the asymmetric unit. This is one of the most important line commands in Olex2.


Complete shown growing bonds:  
$+ html.Snippet(GetVar(default_link),"value=grow -b","hint=grow -b","onclick=grow -b","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows growable "bonds" in a growing mode (see Mode Grow below). Click on any of these bonds to grow the structure.

Mode Grow
$+ html.Snippet(GetVar(default_link),"value=mode grow","hint=mode grow","onclick=mode grow","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Similar to 'grow', but now the 'grow' command will be executed only when an object is clicked. Upon entering a growing mode, growable "bonds" will sprout from atoms satisfying the chosen growing conditions.
There are various modifiers for this command:

Short Contacts:  
$+ html.Snippet(GetVar(default_link),"value=mode grow -s","hint=mode grow -s","onclick=mode grow -s","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows growable "bonds" to atoms involved in "short interactions" (e.g., hydrogen bonds) with the currently displayed structure.


Selection:  
$+ html.Snippet(GetVar(default_link),"value=mode grow -r","hint=mode grow -r","onclick=mode grow -r","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows growable "bonds" to other occurrences of the currently selected atoms.


Van der Waals Radii:  
$+ html.Snippet(GetVar(default_link),"value=mode grow -v 2.0","hint=mode grow -v 2.0","onclick=mode grow -v 2.0","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows growable "bonds" to other occurrences of the currently selected atoms that are at most 2.0 Å away from the selected atom.


Move:  
$+ html.Snippet(GetVar(default_link),"value=mode grow -a","hint=mode grow -a","onclick=mode grow -a","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")When a growable "bond" is clicked, the symmetry-equivalent atom is moved to the new position. This is very useful when trying to assemble a meaningful asymmetric unit for extended structures (polymers).


Shells:  
$+ html.Snippet(GetVar(default_link),"value=mode grow shells","hint=mode grow shells","onclick=mode grow shells","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Shows growable "bonds" that can be clicked to grow the structure outward in concentric shells.

Assemble
Strictly speaking, this tool does not belong to the Grow family of tools, but it is frequently used together with the growing tools. It is used to rearrange components of the asymmetric unit for a more compact or chemically sensible display of the model, often after a 'grow' operation.

Broken Fragments:  
$+ html.Snippet(GetVar(default_link),"value=compaq -a","hint=compaq -a","onclick=compaq -a","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Sometimes, parts of a model may become "broken" - parts that should be bonded are shown as separate fragments. This tool will bring them back together.


Atom-to-Atom:  
$+ html.Snippet(GetVar(default_link),"value=compaq -c","hint=compaq -c","onclick=compaq -c","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")Similar to the Broken Fragments tool, but using a different reassembly algorithm.


Metal Last:  
$+ html.Snippet(GetVar(default_link),"value=compaq -m","hint=compaq -m","onclick=compaq -m","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")In this tool, metal ions are first taken out of the reassembly process (which is very useful when trying to assemble a ligand!), after which they are placed at the shortest possible distance to the other atoms in the structure.


Peaks:  
$+ html.Snippet(GetVar(default_link),"value=compaq -q","hint=compaq -q","onclick=compaq -q","flat=True",td1=, td2=, "fgcolor=#ffffff","bgcolor=GetVar(gui.action_colour)")This moves all electron density peaks as close to existing atoms as possible.

FINISHING

The buttons in this tool tab are for convenient access to elementary versions of more powerful sorting and drawing tools found elsewhere in Olex2.

QUICKSORT

The Sort with Current Settings button sorts the atoms in the model according to the options currently set under the Sorting tool tab. Clicking the pencil icon opens the Sorting tool tab, where the sort settings can be edited.

QUICKIMAGES

The Selected button adds labels to selected atoms and bonds in the model. If nothing is selected, all atoms and bonds will be labelled. The non-H button adds labels to all non-hydrogen atoms, and the No Labels button removes all labels from the model. Clicking the Go button will create an image of the labelled model in the current working folder. To edit all image file options, open the Images tool tab by clicking the pencil icon next to the Go button.

SHIFT-MOVE-TARGET

Move Atoms - Hold down SHIFT - Move atoms with left mouse button Split Atoms - Click on an atom to split it