Macro

Jmol / JSmol Tutorials

• A list of Jmol / JSmol Tutorials written by users.
• Using the mouse (English · Español · Français · Japanese).
• Scripting quickstart: rendering options · selecting atoms.
• How to create surfaces and isosurfaces, including cavities, pockets and tunnels.
• Displaying shapes, polyhedra, orbitals, dipoles, distances, forces and vibrations.
• Creating movies.
• Customizing Jmol: macros · menus.
• Web pages without writing code by using the Jmol "Export to Web" function.

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).

Some examples: (feel free to add your own)

Macro for 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; cartoon off; trace off; ribbon off; color cpk; 
wireframe 0.15; spacefill 20%;

(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.

Macro for 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; spacefill off; wireframe off; cartoon on; color cartoon chain; 
select ligand; wireframe 0.15; spacefill 20%; select all;

(the full script must go in a single line)

Macro to 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 calcium, not (protein, nucleic, water); color [x6DFA36]; 
select solvent; color [x3A79BC]; select temp;

(the full script must go in a single line)

Macro to 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; 

(the full script must go in a single line)

Contributors

AngelHerraez, NicolasVervelle, Remig, Pimpim