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Revision as of 16:00, 24 May 2006 by AngelHerraez (talk | contribs) (Jmol Macro's)
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Jmol Macro's

A Jmol macro is a small script that provides some reusable functionality for the Jmol Application. It is saved as a simple text file, like any other script, in the $HOME/.jmol/macros subdirectory. It will show up in the Macro menu of the Jmol application.

Windows: the $HOME folder's location is stored in the environment variable %USERPROFILE% or in the environment variables %HOMEDRIVE% and %HOMEPATH%; it will usually be at c:\Documents and Settings\(yourUserName)\

If you don't find it, try

My PC > right-click > Properties > Advanced options tab > Environment variables
or open a command line and type set

The macro file is a text file with the extension macro, and its contents must be two lines, starting with "Title=" and "Script=" (only one macro per file).

Example macro:

To show the protein and nucleic acids as cartoons and the ligands as balls-and-sticks, create a text file, write this:

Title=PDB view
Script=select all; spacefill off; wireframe off; cartoon; color cartoon chain; 
select ligand; wireframe 40; spacefill 120

and save as macromol.macro (or the name you like) in the folder $HOME/.jmol/macros

Then to use it, open Jmol application, open menu "Macros", and there you will have a "PDB view" entry.