User:James D Watson/Using Jmol

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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.

There are three main ways for you to interact with protein structures using Jmol:

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.