Jmol/Useful one-liners
From Proteopedia
This is a collection of useful one-liners in Jmol. While the Scene authoring tools give you access to a lot of Jmol's functionality, they don't cover the entire scripting language. However, the SAT contains an input box for entering Jmol commands directly. This page collects commands that might be entered into that textbox to achieve effects not otherwise possible. Viewers of Proteopedia pages might find occasional use of these one-liners as well. To enter them, you first have to right-click on the Jmol window and open a console. For more complex Jmol commands, see Jmol/Using the console.
Examples
Enhancing visibilityhover "%n%R %a"; font hover 30 When spinning is off and you hover over an atom, you get some information. This one-liner increases the font size and condenses the information displayed, showing the one-letter residue name, the residue number and the atom name. set fontScaling ON All labels created after this will scale as you zoom in or out of the structure. select selected and not *%B Deselects alternate conformations. Some models contain two conformations (labeled A and B in column 17 of a PDB file, with fractional occupancies adding up to 1, see e.g. [1]. The example buttons hide or show all representations of alternate conformations. set zshade on This fades the scene (to white if the background is white, to black if the background is black) for atoms further away from the viewer, giving a better 3D feel even when the model is not moving. This command is now available via a control in the SAT. set zshadepower 1 This controls how strongly the scene fades with distance. Color bonds independently from atomscolor bonds green This colors the bonds of the selected atoms, but not the atoms themselves. This is useful to keep the atoms in CPK color scheme (showing which elements we have) while highlighting certain residues or side chains. Saving selections and views for later usedefine aoi selected Defines the currently selected atoms as "aoi". You can use this later in commands such as "select aoi" to select the atoms again. save orientation view1 restore orientation view1
Contactscontact (selected)(not selected) This shows all contacts between the selected atoms and the remainder of the structure, using colored disks to show the contacts and their distances. If you want to exclude covalent bonds, do this contact (selected)(not selected and not within(1.8, selected)) Here is an example of the contacts of one glucose unit in a cellulose model. This used the additional parameter "full" to show pillows (of intersection vanderWaals spheres) instead of disks. Expanding selection to whole residue/groupsselect within(group, selected) This expands the selection to include all atoms belonging to the same residues or groups than the currently selected atoms. [This command is available in the SAT in a perhaps unexpected spot: in the selections tab, in the select within distance box, the second button]. Showing backbone torsion angles phi and psiramachandran selected Not yet categorizedcenter visible
This centers on all atoms that are visible, either explicitly or as part of a cartoon etc. This is also available in the representation tab of the SAT. model all When multiple models are loaded (e.g. NMR structures), or multiple structures are loaded (e.g. superpositions), this shows all the structures at the same time.
Synonyms: zoom 0 Zoom out so that all displayed atoms etc. fit into the window (also centers on visible)
set perspectiveDepth ON Perspective depth shows close objects larger than those far away. Orthoscopic view shows them at the same size. When looking at crystal symmetry, orthoscopic is sometimes preferable. Try it for cellulose structure.
moveto quaternion (61 and mainchain) Orients residue 61 in a specific way. If you use the same command on another amino acid residue, the C-alpha atom and its bonds will be oriented in the same way. This makes it easier to compare side chain conformations.
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