This is the official document. The style is encyclopedic, explaining each command in turn, as usual in reference manuals. In addition to this primary site, with latest updates, there are some mirror sites see links at right. Other Scripts can be included inside the molecular model file.
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This is the official document. The style is encyclopedic, explaining each command in turn, as usual in reference manuals. In addition to this primary site, with latest updates, there are some mirror sites see links at right. Other Scripts can be included inside the molecular model file. See how to do it. Jmol scripting language has grown, among other features, by adding mathematical operators JmolMath , control structures loops, conditionals, etc. You may be interested in this programming language approach.
The command language used by Jmol started with most of the Chime commands, but has outgrown it in a notable extent, allowing for many new capabilities. See Jmol Colors for a comparison. Transversal documentation Covering specific aspects or applications not by command, and usually not exhaustive : Surfaces. Jmol can calculate and render surfaces around a molecule, or part of it, representing its "true" shape and volume. Moreover, isosurfaces, atomic and molecular orbitals, and mathematically defined surfaces can also be rendered.
Persistent and nonpersistent "set" parameters.
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You may save this folder in any convenient location on your computer. Jmol does not need to be "installed", so once these files are in place on your computer, the program will be ready to use. Click on the Jmol. If your computer shows the Jmol. Once a structure has been determined, each atom in the structure is assigned an X,Y,Z coordinate to mark its location in 3-dimensional space. Molecular visualization software, such as Jmol, can then use the coordinates stored in a PDB file to create an interactive 3-dimensional visualization of a molecular structure. We will be using Jmol to view the PDB file 1qys.