$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=arad 0.2","onclick=arad 0.2","flat=False") | Sets the radius of the selected atoms(s) to a value of 0.2 |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=azoom 120","onclick=azoom 120","flat=False") | Scales the selected atom(s) to 120 percent |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=azoom 100","onclick=azoom 100","flat=False") | Scales the selected atom(s) to 100 percent |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=telp 50","onclick=telp 50","flat=False") | Sets the ADP display to a 50 percent probability level |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=telp 30","onclick=telp 30","flat=False") | Sets the ADP display to a 30 percent probability level |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=individualise","onclick=individualise","flat=False") | If you wish to set the radius of a single occurrence of a bond, you must select the bond and type this command first. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grad","onclick=grad","flat=False") | Sets the colour of the four corners of the graduated background. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=panel 0.33","onclick=panel 0.33","flat=False") | The GUI width will adjust as a fraction of the screen width 0.33 will divide Olex2 into 2/3 molecule and 1/3 GUI. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=panel 520","onclick=panel 520","flat=False") | The absolute GUI width in pixels. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=legend","onclick=legend","flat=False") | Switch the legend on or off. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showwindow info","onclick=showwindow info","flat=False") | If selected, more information on a structure is shown in the top panel. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=lines 10","onclick=lines 10","flat=False") | will set the console to only show 10 lines. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=lines -1","onclick=lines -1","flat=False") | will show all lines. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=cell","onclick=cell","flat=False") | Switches the unit cell display on |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=reap","onclick=reap","flat=False") | Open a file via the file browser. This command can be followed by a filename: reap sucrose.ins, for example |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=name \$Q C","onclick=name \$Q C","flat=False") | This will only apply to the currently visible peaks. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=inv -f","onclick=inv -f","flat=False") |
calcCHN() | Calculates the expected values of a CHN analysis from your structure model. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=calcms","onclick=calcms","flat=False") | Simulates a molecular isotope pattern for your structure. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=vvol()","onclick=vvol()","flat=False") | Calculates the molecular volume of the structure. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=calcvol","onclick=calcvol","flat=False") | Calculates the polyhedral volume of a polyheder that is defined by the selected atom. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=wbox","onclick=wbox","flat=False") | A rectangular bounding box is calculated for your molecule and displayed on the screen. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=fvar sel","onclick=fvar sel","flat=False") | The occupancies will be linked such that the individual occupancies add up to unity. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=part -p=2 -lo sel","onclick=part -p=2 -lo sel","flat=False") | The occupancies will be linked such that the individual occupancies add up to unity, and the selected atoms will be added to Parts. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showP 1","onclick=showP 1","flat=False") | Will show only atoms belonging to Part 1. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showP 0 2","onclick=showP 0 2","flat=False") | Will only show atoms that don't belong to a Part and those that belong to Part 2. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showP 0","onclick=showP 0","flat=False") | Will show all atoms. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=himp 0.983","onclick=himp 0.983","flat=False") | Is an example command of this. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -h -l","onclick=labels -h -l","flat=False") | Will show all hydrogen labels. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -l","onclick=labels -l","flat=False") | This will hide all hydrogen labels. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -h -a","onclick=labels -h -a","flat=False") | This will show the AFIX constraints. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=pict fred.png 300","onclick=pict fred.png 300","flat=False") | Creates a png image called fred.png with a width of 300px |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=pictPR filename.pov","onclick=pictPR filename.pov","flat=False") | Saves the popvray output file 'filename.pov' |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=help calcvoid","onclick=help calcvoid","flat=False") |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=calcsolv","onclick=calcsolv","flat=False") | Calculates the solvent accessible voids. This calculation is based on the smtbx/cctbx Olex2 libraries. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=fuse","onclick=fuse","flat=False") | Unmatches the structure |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=pers","onclick=pers","flat=False") | Atoms are shown as spheres. The size of the sphere depends on the radius of the atom type represented by the sphere. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=telp n","onclick=telp n","flat=False") where default n = 50% | Aniosotropic atoms are shown as ellipsoids. Isotropic atoms are shown as spheres, who'se size depends on the value of the Uiso of the individual atom represented by the sphere. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=proj","onclick=proj","flat=False") | The structure is shown as a wireframe. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sfil","onclick=sfil","flat=False") | Atoms are represented as space-filling spheres. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=tubes","onclick=tubes","flat=False") | Atoms are represented as connected tubes. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=default","onclick=default","flat=False") | All display settings are reset to the default values. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mask atoms 37","onclick=mask atoms 37","flat=False") | Shows the structure in a polyhedral representation. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=rota 2 -10.2","onclick=rota 2 -10.2","flat=False") | This will rotate the structure around the y axis by -10.2 degrees. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode move","onclick=mode move","flat=False") |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode move -c","onclick=mode move -c","flat=False") |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq","onclick=compaq","flat=False") , $+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -a","onclick=compaq -a","flat=False") | In cases where parts of your structure have become fragmented or 'disjointed', this command will re-assemble the fragments. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=move","onclick=move","flat=False") | All moieties in the structure will be centred on the cell. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=move","onclick=move","flat=False") | All moieties in the structure will be centred on the largest moiety. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=basis","onclick=basis","flat=False") | Displays/Hides the basis vectors of this structure. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=cell","onclick=cell","flat=False") | Displays/Hides a drawing of the unit cell. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=qual -l","onclick=qual -l","flat=False") , $+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=qual -m","onclick=qual -m","flat=False") , $+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=qual -h","onclick=qual -h","flat=False") | Changes the quality setting in which atoms are drawn. A lower quality can be useful if the computer struggles with larger structures. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=fuse","onclick=fuse","flat=False") | Display the asymmetric unit of the structure only. All symmetry generated atoms will be removed. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow","onclick=grow","flat=False") | All symmetry equivalent atoms that are required to show the 'complete' structure will be generated. Of course, in the case of polymeric structures, this is somewhat arbitrary, and more controlled growing conditions will need to be employed. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow","onclick=grow","flat=False") | All 'missing' connected symmetry equivalent atoms will be generated. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow -s","onclick=grow -s","flat=False") | This will grow atoms shell-by-shell from the currently displayed image. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow -w","onclick=grow -w","flat=False") | This will generate all missing symmetry equivalent atoms of an already grown structure, independent of whether these are bound to the main fragment or not. In other words: all solvent molecules and counter-ion will be generated according to what is already shown. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=fuse","onclick=fuse","flat=False") | Removes all symmetry equivalent atoms and displays the asymmetric unit. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow -b","onclick=grow -b","flat=False") | If you are in a growing mode, then clickable growing bonds will be shown. All of these can be grown |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow","onclick=mode grow","flat=False") | Similar to grow, but now this command will be executed only after you click on an object. When you enter a growing mode, clickable 'growing bonds' will sprout from atoms where the kind of growing you have asked for is applicable. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow -r","onclick=mode grow -r","flat=False") | Will show growable 'bonds' to other occurances of the currently selected atoms. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow -v 2.0","onclick=mode grow -v 2.0","flat=False") | Will show growable 'bonds' to other occurances of the currently selected atoms that are at least the indicated distance away from the selected atom. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow -a","onclick=mode grow -a","flat=False") | when you click on growable bonds the symmetry equivalent atom will be moved to the new position. This is really useful when you are trying to assemble a meaningful asymmetric unit for extended structures (polymers). |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow -s","onclick=grow -s","flat=False") | This will grow atoms shell-by-shell from the currently displayed image. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -a","onclick=compaq -a","flat=False") | Sometimes, your structure may become 'broken' - parts that should be bonded are shown as separate fragments. This tool will bring them back together. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -c","onclick=compaq -c","flat=False") | Similar to the 'Broken Fragments' tool, but a different algorithm is used. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -m","onclick=compaq -m","flat=False") | In this tool, metal ions are taken out of the equation at first (which is very useful when trying to assemble a ligand!) and then the metal ion is placed at the shortest possible distance. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -q","onclick=compaq -q","flat=False") | This will move all electron density peaks as closely to existing atoms as possible. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=name sel type","onclick=name sel type","flat=False") | Will change all currently selected atoms into the new type. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=name sel integer","onclick=name sel integer","flat=False") | Will re-number all currently selected atoms in the order of which they were selected starting from. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=match sel -n=suffix","onclick=match sel -n=suffix","flat=False") | Enter a suffix character into the box, then click the link.This will transfer the naming scheme of the first molecule to the second molecule with the suffix letter you have chosen. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=suffix'>match sel -n=\$suffix","onclick=suffix'>match sel -n=\$suffix","flat=False") | Instead of merely adding a suffix, you can also replace the first character of the original naming scheme with another character. This is useful, for example, if you wish to name all atoms in one ligand like C101, C102, C102 ... and corresponding atoms in the other ligand like C201, C202, C203 ... |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=suffix'>match sel -n=-suffix","onclick=suffix'>match sel -n=-suffix","flat=False") | Equally, the last character of an atom name can be replaced |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=weight","onclick=weight","flat=False") | A weighting scheme should be applied to your data. This is usually done when your model is finished. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel \$c","onclick=sel \$c","flat=False") | Selects all C atoms |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel -u","onclick=sel -u","flat=False") | Deselects everything |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel c1","onclick=sel c1","flat=False") | Selects C1 |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel \$c \$n","onclick=sel \$c \$n","flat=False") | Selects all C and N atoms |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel -i","onclick=sel -i","flat=False") | Inverts the current selection. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel -u","onclick=sel -u","flat=False") | Deselects (unselects) the all selected atoms. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=kill sel","onclick=kill sel","flat=False") | Deletes all selected atoms. Same as pressing the 'Delete' key. Undo with CTRL+Z. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=selback","onclick=selback","flat=False") | Re-select all atoms of the previous selection. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sg","onclick=sg","flat=False") | Olex2 can also determine the space group. Press the 'Suggest SG' link and the most likely choices will appear in the drop-down box on the right. You can type 'text' to see the full output of the data analysis. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=help labels","onclick=help labels","flat=False") | To see all the command line options for the labels |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -l","onclick=labels -l","flat=False") | All atom names of non-hydrogen atoms will be displayed next to the atoms. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -o","onclick=labels -o","flat=False") | This displays the crystallographic occupancy of any atoms which are not 100% occupied i.e. their occupancy is not 1. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -co","onclick=labels -co","flat=False") | Displays the 'chemical occupancy' on the labels. Basically, the occupancy values for atoms that are located on symmetry elements are not shown. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -p","onclick=labels -p","flat=False") | Displays PART numbers for any atoms not in PART 0. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -lo","onclick=labels -lo","flat=False") | If atoms are linked, the link code will be shown. (FVAR 21/-21 in ShelXL language) |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -h -l","onclick=labels -h -l","flat=False") | This will include the hydrogen atom labels along with the atom name and Q-peak labels |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -v","onclick=labels -v","flat=False") | Displays any atoms where the occupancy is linked to any variable |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -a -h","onclick=labels -a -h","flat=False") | This is useful to check the AFIX commands that are being applied to the structure |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -qi","onclick=labels -qi","flat=False") | Relative intensities of the Q-peaks will be displayed on the structure |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -rn","onclick=labels -rn","flat=False") | Show the number of the residue an atom belongs to |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=labels -rc","onclick=labels -rc","flat=False") | Show the number of the residue class an atom belongs to |
$spy.MakeElementButtonsFromFormula('mode') | All atoms present in the model are shown. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=name sel C","onclick=name sel C","flat=False") | Turns all selected atoms into carbon |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode name C","onclick=mode name C","flat=False") | Mode, where subsequently clicked atoms will turn into carbon atoms |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=name \$Q C","onclick=name \$Q C","flat=False") | Turns all Q-peaks into carbon atoms |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=hadd","onclick=hadd","flat=False") | Adds hydrogen atoms to all selected atoms (or all, if none selected) |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=hadd 137","onclick=hadd 137","flat=False") | Will use specifed AFIX if possible. (137 adds three hydrogen atoms to a methl group, for example. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=hadd -137","onclick=hadd -137","flat=False") | If the connectivity does not allow the addition of the specified AFIX atoms, it is still possible to place them in this way. Two atoms must be selected to denote a vector, with the atom to which hydrogen atoms are to be added selected first |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=isot","onclick=isot","flat=False") | All selected atoms will be refined isotropically |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=anis","onclick=anis","flat=False") | All selected atoms will be refined anisotropically (ellipsoids will result) |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=name \$Q C","onclick=name \$Q C","flat=False") | $spy.MakeHoverButton('toolbar-QC','name \$Q C') | This tool will change all visible electron density peaks to Carbon atoms, regardless of the peak height. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=name \$Q H","onclick=name \$Q H","flat=False") | $spy.MakeHoverButton('toolbar-QH','name \$Q H') | All visible Q-peaks will be turned into Hydrogen atoms |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=clean","onclick=clean","flat=False") | $spy.MakeHoverButton('toolbar-tidy','clean') | Tidy the Structure: Small and geometrically impossible peaks will be removed, all remaining peaks will be turned into Carbon. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=kill \$H","onclick=kill \$H","flat=False") | $spy.MakeHoverButton('toolbar-killH','kill \$H') | Deletes all selected Hydrogen atoms from your structure. If no hydrogen atoms are selected, all will be deleted. Undo with Ctr+Z. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showQ","onclick=showQ","flat=False") | $spy.MakeHoverButton('toolbar-Q','showQ') | CTRL+Q. Toggle between three states: Show electron density peaks, show them with bonds or hide them. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showH","onclick=showH","flat=False") | $spy.MakeHoverButton('toolbar-H','showH') | CTRL+H. Toggle between three states: Show H atoms, show them with H-bonds or hide them. Hydrogen atoms remain in the model. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq>>compaq-a>>center","onclick=compaq>>compaq-a>>center","flat=False") | $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. For a molecular structure this is typically the sum formula of the molecule. If there are two independent molecules on the screen, Z' must be set to 2. If the molecule needs to be grown, Z' will smaller than one (often 0.5). |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=fixunit","onclick=fixunit","flat=False") | $spy.MakeHoverButton('toolbar-OK','fixunit') | Adjusts the sum formula to what is currently present in the model, taking the value of Z' into account. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showp 0 1","onclick=showp 0 1","flat=False") | Shows all atoms in no particular part and all atoms in PART 1 |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showp 0 2","onclick=showp 0 2","flat=False") | Shows all atoms in no particular part and all atoms in PART 2 |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showp 1","onclick=showp 1","flat=False") | Shows only the atoms PART 1 |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=showp","onclick=showp","flat=False") | Show all parts |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel part 1","onclick=sel part 1","flat=False") | Selects all atoms in PART 1 |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode split","onclick=mode split","flat=False") | Splits subsequently clicked atoms |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode split -r=EADP","onclick=mode split -r=EADP","flat=False") | This will split the atom as above, but will restrain the ADP values for both atoms to be the same. This is useful early on, and should probably be removed once the disorder model is nearly complete. You might want to apply the DELU restraint instead. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode split -r=ISOR","onclick=mode split -r=ISOR","flat=False") | This will split the atom as above, and reply an ISOR restraint to each of the two atoms. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode split -r=SIMU","onclick=mode split -r=SIMU","flat=False") | As above, but with a SIMU restraint. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=CalcFourier","onclick=CalcFourier","flat=False") | Calculates the map according to the settings set in the map tool. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel atoms where xatom.uiso > 0.06 xatom.type!='Q'","onclick=sel atoms where xatom.uiso > 0.06 xatom.type!='Q'","flat=False") |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=sel atoms where xatom.uiso > 0.08","onclick=sel atoms where xatom.uiso > 0.08","flat=False") | Selects all atoms where the Uiso value is larger than 0.08 |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow","onclick=grow","flat=False") | All 'missing' connected symmetry equivalent atoms will be generated. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow -s","onclick=grow -s","flat=False") | This will grow atoms shell-by-shell from the currently displayed image. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow -w","onclick=grow -w","flat=False") | This will generate all missing symmetry equivalent atoms of an already grown structure, independent of whether these are bound to the main fragment or not. In other words: all solvent molecules and counter-ion will be generated according to what is already shown. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=fuse","onclick=fuse","flat=False") | Removes all symmetry equivalent atoms and displays the asymmetric unit. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=grow -b","onclick=grow -b","flat=False") | If you are in a growing mode, then clickable growing bonds will be shown. All of these can be grown |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow","onclick=mode grow","flat=False") | Similar to grow, but now this command will be executed only after you click on an object. When you enter a growing mode, clickable 'growing bonds' will sprout from atoms where the kind of growing you have asked for is applicable. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow -s","onclick=mode grow -s","flat=False") | Will show these growable 'bonds' to those atoms where 'short interactions' exist. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow -r","onclick=mode grow -r","flat=False") | Will show growable 'bonds' to other occurances of the currently selected atoms. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow -v 2.0","onclick=mode grow -v 2.0","flat=False") | Will show growable 'bonds' to other occurances of the currently selected atoms that are at least the indicated distance away from the selected atom. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=mode grow -a","onclick=mode grow -a","flat=False") | When you click on growable bonds the symmetry equivalent atom will be moved to the new position. This is really useful when you are trying to assemble a meaningful asymmetric unit for extended structures (polymers). |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -a","onclick=compaq -a","flat=False") | Sometimes, your structure may become 'broken' - parts that should be bonded are shown as separate fragments. This tool will bring them back together. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -c","onclick=compaq -c","flat=False") | Similar to the 'Broken Fragments' tool, but a different algorithm is used. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -m","onclick=compaq -m","flat=False") | In this tool, metal ions are taken out of the equation at first (which is very useful when trying to assemble a ligand!) and then the metal ion is placed at the shortest possible distance. |
$+ html.Snippet("S:\olex2-trunk\util\pyUtil\PluginLib\plugin-GitHelp\gui-link","value=compaq -q","onclick=compaq -q","flat=False") | This will move all electron density peaks as closely to existing atoms as possible. |