Difference between revisions of "Macro"

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(new macro example and reorganize titles)
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{{Tutorials_Sections}}
 
{{Tutorials_Sections}}
=== Introduction to macros in Jmol application ===
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= 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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contents must be two lines, starting respectively 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).
  
Some examples:
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 +
= Example macros =
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''(feel free to add your own)''
 
''(feel free to add your own)''
  
== Macro for balls & sticks ==
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== Balls & sticks ==
 
To show everything as balls-and-sticks in CPK color, create a text file with this contents:
 
To show everything as balls-and-sticks in CPK color, create a text file with this contents:
 
<pre>
 
<pre>
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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.
  
== Macro for macromolecules, PDB style ==
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== 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:
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: (the full script must go in a single line)
 
: (the full script must go in a single line)
  
== Macro to color according to DRuMS MacroMicro scheme ==
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== Color according to DRuMS MacroMicro scheme ==
 
To color the current selection 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>
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: (the full script must go in a single line)
 
: (the full script must go in a single line)
  
== Macro to get current orientation ==
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== Get current orientation ==
 
This would be useful to copy and paste the current orientation of the model into your script.
 
This would be useful to copy and paste the current orientation of the model into your script.
 
<pre>
 
<pre>
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Script=show orientation moveTo;  
 
Script=show orientation moveTo;  
 
</pre>
 
</pre>
: (the full script must go in a single line)
 

Revision as of 11:09, 22 July 2008

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).


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; 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.

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)

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)

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;