Jmol/Useful one-liners

Enhancing visibility

hover "%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 atoms

color 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 use

define 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

Contacts

contact (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 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/groups

select 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 psi

ramachandran selected

Not yet categorized

center 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: model 0, frame all, frame 0

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.