Macro - Revision history

Remig at 14:52, 24 July 2014

2014-07-24T14:52:25Z

AngelHerraez: update scripts to current Jmol abilities

2012-07-26T15:07:08Z

update scripts to current Jmol abilities

AngelHerraez at 11:09, 22 July 2008

2008-07-22T11:09:48Z

AngelHerraez: new macro example and reorganize titles

2008-07-22T11:02:46Z

new macro example and reorganize titles

NicolasVervelle: Reverted edits by Lo5Wga (Talk); changed back to last version by NicolasVervelle

2007-06-11T20:34:11Z

Reverted edits by Lo5Wga (Talk); changed back to last version by NicolasVervelle

Anonymous at 02:46, 11 June 2007

2007-06-11T02:46:11Z

NicolasVervelle: Reverted edits by TqzS2e (Talk); changed back to last version by Pimpim

2007-06-10T17:33:33Z

Reverted edits by TqzS2e (Talk); changed back to last version by Pimpim

Anonymous at 13:24, 10 June 2007

2007-06-10T13:24:26Z

Pimpim: added tutorials sections template

2007-06-06T17:52:10Z

added tutorials sections template

AngelHerraez: /* Jmol Macro's */

2006-05-24T16:51:49Z

‎Jmol Macro's

← Older revision		Revision as of 14:52, 24 July 2014
Line 16:		Line 16:
	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).

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

	= Example macros =		= Example macros =

@@ Line 25: / Line 25: @@
 <pre>
 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%;
 </pre>
 : (the full script must go in a single line)
@@ Line 39: / Line 38: @@
 <pre>
 Title=PDB view
-Script=select all; spacefill off; wireframe off; cartoon on; color cartoon chain;
+Script=select all; cartoon only; color cartoon chain;
-select ligand; wireframe 0.15; spacefill 20%; select all;
+select ligand; wireframe 0.15; spacefill 23%; select all;
 </pre>
 : (the full script must go in a single line)
@@ Line 50: / Line 49: @@
 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 ligand; color [x6DFA36]; select solvent; color [x3A79BC];
-select solvent; color [x3A79BC]; select temp;
+select temp;
 </pre>
 : (the full script must go in a single line)

@@ Line 1: / Line 1: @@
 {{Tutorials_Sections}}
-=== Introduction to macros in Jmol application ===
+= 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.
@@ Line 16: / Line 16: @@
 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 ==
+== Balls & sticks ==
 To show everything as balls-and-sticks in CPK color, create a text file with this contents:
 <pre>
@@ Line 32: / Line 34: @@
 Then to use it, open Jmol application, open menu "Macros", and there you will have a "Ball & Stick" entry.
-== Macro for macromolecules, PDB style ==
+== Macromolecules, PDB style ==
 To show the protein and nucleic acids as cartoons and the ligands as
 balls-and-sticks:
@@ Line 42: / Line 44: @@
 : (the full script must go in a single line)
-== Macro to color according to DRuMS MacroMicro scheme ==
+== 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):
 <pre>
@@ Line 53: / Line 55: @@
 : (the full script must go in a single line)
-== Macro to get current orientation ==
+== Get current orientation ==
 This would be useful to copy and paste the current orientation of the model into your script.
 <pre>
@@ Line 59: / Line 61: @@
 Script=show orientation moveTo;
 </pre>

@@ Line 1: / Line 1: @@
 {{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.
@@ Line 14: / Line 14: @@
 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==
+Some examples:
-To show everything as balls-and-sticks, CPK color, create a text file, write this:
+''(feel free to add your own)''
 <pre>
 Title=Ball & Stick
 Script=select all; cartoon off; trace off; ribbon off; color cpk;
-wireframe 40; spacefill 120
+wireframe 0.15; spacefill 20%;
 </pre>
 : (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.
-==Example macro 2==
+== Macro for macromolecules, PDB style ==
 To show the protein and nucleic acids as cartoons and the ligands as
 balls-and-sticks:
 <pre>
 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 40; spacefill 120
+select ligand; wireframe 0.15; spacefill 20%; select all;
 </pre>
 : (the full script must go in a single line)
-==Example macro 3==
+== Macro to 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>
 Title=color MacroMicro
@@ Line 46: / Line 49: @@
 select dna; color [xAE00FE]; select rna; color [xFD0162];
 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)

@@ Line 19: / Line 19: @@
 To show everything as balls-and-sticks, CPK color, create a text file, write this:
 <pre>
-Title=Ball
+Title=Ball & Stick

← Older revision		Revision as of 17:52, 6 June 2007
Line 1:		Line 1:
		+	{{Tutorials_Sections}}
	=== Jmol Macro's ===		=== Jmol Macro's ===

@@ Line 3: / Line 3: @@
 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|$HOME/.jmol/macros}} subdirectory. It will show up in the Macro menu of the Jmol application.
 '''Windows''': the {{Directory|$HOME}} folder's location is stored in the environment variable <code>%USERPROFILE%</code> or in the environment variables <code>%HOMEDRIVE%</code> and <code>%HOMEPATH%</code>; it will usually be at
 <code>c:\Documents and Settings\(yourUserName)\</code>
 If you don't find it, try
-: My PC > right-click > Properties > Advanced options tab > Environment variables
+: My PC > right-click > Properties > Advanced Options (tab) > Environment Variables (button)
 : or open a command line and type <code>set</code>
-The macro file is 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).
 ==Example macro 1==