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User:James D Watson/Using Jmol
From Proteopedia
Introduction to Jmol
Jmol is a commonly used molecular graphics viewer. The aim of this tutorial is to provide you with an introduction to some of the common manipulations to help you understand protein structure data.
- the mouse
- the menu
- the console
The Mouse
The three elementary ways to interact with the molecule in the viewer are:- Rotation
- Translation
- Zooming
The most basic interaction with a molecule involves rotating it around in the viewer. To freely rotate the molecule yourself, left-click and drag on it. Drag the cursor up and down for x-axis rotation, left-right for y-axis rotation.
Occasionally it is necessary to translocate the protein along an axis. In order to do so yourself, hold down shift, then double-click and drag on the structure. You will see the molecule follow your mouse movements (up, down, left and right).
It is common to zoom in on particular aspects of a molecule. To zoom the molecule yourself, shift-click and drag. Drag the cursor down to zoom in, drag it up to zoom out.
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| 3cin, resolution 1.70Å () | |||||||||
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| Ligands: | , , | ||||||||
| Gene: | TM1419, TM_1419 (Thermotoga maritima MSB8) | ||||||||
| Activity: | Inositol-3-phosphate synthase, with EC number 5.5.1.4 | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum, TOPSAN | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
