| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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 ' |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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'. |
| $+ 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 ' |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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°. |
| $+ 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)") |
| $+ 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)") |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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 ' |
| $+ 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., ' |
| $+ 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 ' |
| $+ 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, ' |
| $+ 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 ... |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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 ' |
| $+ 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. |
| $+ 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. |
| $+ 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 ' |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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). |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $spy.MakeElementButtonsFromFormula('mode') | All atoms present in the model are shown. The '...' button opens the Periodic Table if more elements need to be added. |
| $+ 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. |
| $+ 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. |
| $+ 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). |
| $+ 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). |
| $+ 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 ' |
| $+ 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') | ' |
| $+ 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') | ' |
| $+ 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. |
| 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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 ' |
| $+ 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. |
| $+ 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. |
| $+ 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 ' |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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). |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |
| $+ 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. |