Jmol/Using the console

The Jmol console may be used to obtain information, and to change the scene currently displayed. This may be useful while viewing a Proteopedia page, or while creating a 3D scene, achieving certain effects not possible with the Scene Authoring Tools alone. You can open the Jmol console via the right-click menu in the Jmol window, or via a dedicated button under the Jmol window in the SAT.

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

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, . 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, , and the Jmol commands used.

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis