Jmol/Using the console

Obtaining information

show sequence

This shows the residues that contain selected atoms

show selected

This shows which atoms are selected

show coordinates

This shows the coordinates of selected atoms

show measurements

This shows all the distances and angles that are displayed

Changing the scene

Surfaces

The "isosurface" command in Jmol draws all kind of surfaces (molecular surface, electron density, orbitals) with all kinds of coloring options (by atom, electrostatic potential, conservation, distance, etc.). It is a complex command, so examples help to learn how to use it.

Ammonia with lone pair cartoon

electrostatic potential of water

Electron density

The way electron density is usually shown is as surface, but it warrants its own category because getting the electron density data is a special topic (also discussed at User:Karsten Theis/Electron density.

Superpositions

For a Jmol/superposition, you load a file that contains multiple models, or a structure with multiple copies of the same chain in the asymmetric unit. The example below is for multiple models, with model 1.1 and 2.1 sufficiently similar to be meaningfully superimposed. The three dots ("...") in the two select statements should be filled in such that equivalent atoms are selected. In the example scene below, both structures bind to the same ligand.

select 1.1 and ...
show selected
define set1 selected
select 2.1 and ...
show selected
define set2 selected
compare {2.1} {1.1} ATOMS{set2}{set1} ROTATE TRANSLATE

Model 2.1 gets moved and model 1.1 stays in place.

Here is an example, GAL and NAGAL superimposed via the ligand. The Jmol script for the scene is here (see Figure X), and the key command is:

"compare {2.1} {1.1} ATOMS{1000:A and _C}{801:A and _C} ROTATE TRANSLATE"

Use the following buttons to explore the example scene:

Covalent modifications

This script shows carbohydrates and the protein side chains that are covalently linked to them as wireframe.

select within(1.8, carbohydrate) and protein
show selected
select within(group, selected)
select selected and (sidechain or alpha)
select selected or carbohydrate
wireframe on

Because bonds of side chains and modifications are drawn in a single command, the covalent links between them will also be drawn.

Here is an example, galactosidase, and the Jmol commands used.