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Jmol Tutorials


Introduction to macros in Jmol application

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 (button)
or open a command line and type set

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

Example macros

(feel free to add your own)

Balls & sticks

To show everything as balls-and-sticks in CPK color, create a text file with this contents:

Title=Ball & Stick
Script=select all; color cpk; wireframe only; wireframe 0.15; spacefill 23%;
(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.

Macromolecules, PDB style

To show the protein and nucleic acids as cartoons and the ligands as balls-and-sticks:

Title=PDB view
Script=select all; cartoon only; color cartoon chain; 
select ligand; wireframe 0.15; spacefill 23%; select all;
(the full script must go in a single line)

Color according to DRuMS MacroMicro scheme

To color the current selection 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 ligand; color [x6DFA36]; select solvent; color [x3A79BC]; 
select temp;
(the full script must go in a single line)

Get current orientation

This would be useful to copy and paste the current orientation of the model into your script.

Title=get orientation
Script=show orientation moveTo; 
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