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.

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D 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.

Proteopedia Page Contributors and Editors (what is this?)

Karsten Theis