Macro
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 1
To show everything as balls-and-sticks, CPK color, create a text file, write this:
Title=Ball & Stick Script=select all; cartoon off; trace off; ribbon off; color cpk; wireframe 40; spacefill 120
- (the full script must go in a single line)
and save as ballandstick.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 "Ball & Stick" entry.
Example macro 2
To show the protein and nucleic acids as cartoons and the ligands as balls-and-sticks:
Title=PDB view Script=select all; spacefill off; wireframe off; cartoon; color cartoon chain; select ligand; wireframe 40; spacefill 120
- (the full script must go in a single line)
Example macro 3
To color everything using DRuMS "macromolecule" color scheme (slightly adapted to account for Jmol's capabilities):
Title=color MacroMicro Script=define temp selected; select protein; color [xCBBE8A]; select dna; color [xAE00FE]; select rna; color [xFD0162]; select calcium, not (protein, nucleic, water); color [x6DFA36]; select solvent; color [x3A79BC]; select temp
- (the full script must go in a single line)
