Difference between revisions of "Macro"

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{{Tutorials_Sections}}
 
{{Tutorials_Sections}}
=== Jmol Macro's ===
+
= 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 {{Directory|$HOME/.jmol/macros}} subdirectory. It will show up in the Macro menu of the 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 {{Directory|$HOME/.jmol/macros}} subdirectory. It will show up in the Macro menu of the Jmol application.
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The macro file must be a text file with the extension <code>macro</code>, and its  
 
The macro file must be a text file with the extension <code>macro</code>, and its  
contents must be two lines, starting with "Title=" and "Script=" (only one macro per file).
+
contents must be two lines, starting respectively with "Title=" and "Script=" (only one macro per file).
  
==Example macro 1==
+
Note that macros will be listed in the Jmol application Macros menu alphabetically by file name, not by title.
To show everything as balls-and-sticks, CPK color, create a text file, write this:
+
 
 +
= 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:
 
<pre>
 
<pre>
 
Title=Ball & Stick
 
Title=Ball & Stick
Script=select all; cartoon off; trace off; ribbon off; color cpk;  
+
Script=select all; color cpk; wireframe only; wireframe 0.15; spacefill 23%;
wireframe 40; spacefill 120
 
 
</pre>
 
</pre>
 
: (the full script must go in a single line)
 
: (the full script must go in a single line)
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Then to use it, open Jmol application, open menu "Macros", and there you will have a "Ball & Stick" entry.
 
Then to use it, open Jmol application, open menu "Macros", and there you will have a "Ball & Stick" entry.
  
==Example macro 2==
+
== Macromolecules, PDB style ==
 
To show the protein and nucleic acids as cartoons and the ligands as  
 
To show the protein and nucleic acids as cartoons and the ligands as  
 
balls-and-sticks:
 
balls-and-sticks:
 
<pre>
 
<pre>
 
Title=PDB view
 
Title=PDB view
Script=select all; spacefill off; wireframe off; cartoon; color cartoon chain;  
+
Script=select all; cartoon only; color cartoon chain;  
select ligand; wireframe 40; spacefill 120
+
select ligand; wireframe 0.15; spacefill 23%; select all;
 
</pre>
 
</pre>
 
: (the full script must go in a single line)
 
: (the full script must go in a single line)
  
==Example macro 3==
+
== Color according to DRuMS MacroMicro scheme ==
To color everything using [http://www.umass.edu/molvis/drums/ DRuMS] "macromolecule" color scheme (slightly adapted to account for Jmol's capabilities):
+
To color the current selection using [http://www.umass.edu/molvis/drums/ DRuMS] "macromolecule" color scheme (slightly adapted to account for Jmol's capabilities):
 
<pre>
 
<pre>
 
Title=color MacroMicro
 
Title=color MacroMicro
 
Script=define temp selected; select protein; color [xCBBE8A];  
 
Script=define temp selected; select protein; color [xCBBE8A];  
 
select dna; color [xAE00FE]; select rna; color [xFD0162];  
 
select dna; color [xAE00FE]; select rna; color [xFD0162];  
select calcium, not (protein, nucleic, water); color [x6DFA36];  
+
select ligand; color [x6DFA36]; select solvent; color [x3A79BC];  
select solvent; color [x3A79BC]; select temp
+
select temp;
 
</pre>
 
</pre>
 
: (the full script must go in a single line)
 
: (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.
 +
<pre>
 +
Title=get orientation
 +
Script=show orientation moveTo;
 +
</pre>

Latest revision as of 14:52, 24 July 2014

Jmol / JSmol 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).

Note that macros will be listed in the Jmol application Macros menu alphabetically by file name, not by title.

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;