Difference between revisions of "Macro"
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m (Reverted edits by Lo5Wga (Talk); changed back to last version by NicolasVervelle) |
AngelHerraez (talk | contribs) (new macro example and reorganize titles) |
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{{Tutorials_Sections}} | {{Tutorials_Sections}} | ||
| − | === Jmol | + | === 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. | ||
| Line 14: | Line 14: | ||
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). |
| − | == | + | Some examples: |
| − | To show everything as balls-and-sticks | + | ''(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: | ||
<pre> | <pre> | ||
Title=Ball & Stick | Title=Ball & Stick | ||
Script=select all; cartoon off; trace off; ribbon off; color cpk; | Script=select all; cartoon off; trace off; ribbon off; color cpk; | ||
| − | wireframe | + | wireframe 0.15; spacefill 20%; |
</pre> | </pre> | ||
: (the full script must go in a single line) | : (the full script must go in a single line) | ||
| Line 29: | Line 32: | ||
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 == |
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; spacefill off; wireframe off; cartoon on; color cartoon chain; |
| − | select ligand; wireframe | + | select ligand; wireframe 0.15; spacefill 20%; select all; |
</pre> | </pre> | ||
: (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 == |
| − | To color | + | 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 | ||
| Line 46: | Line 49: | ||
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 calcium, not (protein, nucleic, water); color [x6DFA36]; | ||
| − | select solvent; color [x3A79BC]; select temp | + | select solvent; color [x3A79BC]; select temp; |
| + | </pre> | ||
| + | : (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. | ||
| + | <pre> | ||
| + | Title=get orientation | ||
| + | Script=show orientation moveTo; | ||
</pre> | </pre> | ||
: (the full script must go in a single line) | : (the full script must go in a single line) | ||
Revision as of 11:02, 22 July 2008
- 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.
Contents
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 atc:\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)
