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.

view1 = script("show moveto")

Saves the current orientation in the variable "view1". Later, you can go back to this view using:

script inline @view1

Not yet categorized

center visible

This centers on all atoms that are visible, either explicitly or as part of a cartoon etc.

model 0

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.