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
%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
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).
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.