Running Scripts - Revision history

Bell: 5 revisions

2014-03-28T03:49:32Z

5 revisions

Speleo3: Modules

2011-12-14T17:10:21Z

Modules

Karo at 11:20, 5 August 2010

2010-08-05T11:20:34Z

Karo at 11:20, 5 August 2010

2010-08-05T11:20:13Z

Karo at 11:05, 5 August 2010

2010-08-05T11:05:42Z

Karo: Help for running pymol and python scripts for beginners

2010-08-05T09:46:34Z

Help for running pymol and python scripts for beginners

New page

This page is a short description for beginners on how to run scripts in PyMOL, e.g. from the [[:Category:Script_Library|Script Library]]. For help on writing scripts, look here: [[Simple_Scripting]], [[Advanced_Scripting]].

== Saving the source code ==

First, you have to save the source code. Copy the text in the box to a
text editor and save it in text format under an arbitrary file name,
let's say we save it as script.txt in the PyMOL working directory.

== Python or Pymol? ==

Then, you have to find out wheter the script you want to run is a
python script or a PyMOL script. Look at the source code: if the lines
look just as you type them in the command line in PyMOL, it is a PyMOL
script. Run it with @, in our example, type

<source lang="python">
@script.txt
</source>

in the PyMOL command line. You can find examples in the script library:
[[Split_Movement]] (loads a structure from the internet and moves parts in different directions),
[[Show_charged]] (Selects charged residues and highlights them).
Any PyMOL log file would also be an example for a pymol script.

If, in contrast, you find words as "import" in one of the first lines,
or "def" or "cmd" in the text body, you have a python script. Run it
with run. In the example, type

<source lang="python">
run script.txt
</source>

in the PyMOL command line.

Most python scripts in the script library don't start action
immediately but define a new command instead. You first have to run
the script and then you can use the command. Many script pages provide
hints for usage. If not, look at the bottom of the script for a line like this:

<source lang="python">
cmd.extend("new_command",new_command)
</source>

The text in quotation marks is the new command. Enter it in the PyMOL command line.

You can find many examples for python scripts in the script library, e.g.:
[[Color_Objects]] (colors all the objects differently)
[[Resicolor]] (Colors residues according to their property)

== Example: Color_Objects ==

<source lang="python">
PyMOL>run color_obj.py
PyMOL>color_obj

Colouring objects using PyMOL defined colours

obj_0001 red
obj_0002 green
obj_0003 blue
obj_0004 yellow
obj_0005 violet
obj_0006 cyan
obj_0007 salmon
obj_0008 lime
obj_0009 pink
obj_0010 slate
obj_0011 magenta
obj_0012 orange
obj_0013 marine
obj_0014 olive
...
</source>

← Older revision		Revision as of 17:10, 14 December 2011
Line 48:		Line 48:
	[[Resicolor]] (Colors residues according to their property)		[[Resicolor]] (Colors residues according to their property)

		+	== Python Modules ==

		+	A python '''module''' is a python script that runs in it's own namespace, by using the '''import''' syntax instead of '''run'''. The file must be located in any directory of the [http://docs.python.org/library/sys.html#sys.path sys.path] variable. This is the recommended way for scripts from the [[Git intro\|Pymol-script-repo]].
		+
		+	<source lang="python">
		+	import color_obj # skip the .py extension!
		+	</source>

	== Example: Color_Objects ==		== Example: Color_Objects ==

← Older revision		Revision as of 11:20, 5 August 2010
Line 1:		Line 1:
	This page is a short description for beginners on how to run scripts in PyMOL, e.g. from the [[:Category:Script_Library\|Script Library]]. For help on writing scripts, look here: [[Simple_Scripting]], [[Advanced_Scripting]].		This page is a short description for beginners on how to run scripts in PyMOL, e.g. from the [[:Category:Script_Library\|Script Library]]. For help on writing scripts, look here: [[Simple_Scripting]], [[Advanced_Scripting]].
−

	== Saving the source code ==		== Saving the source code ==

← Older revision		Revision as of 11:05, 5 August 2010
Line 77:		Line 77:
	...		...
	</source>		</source>
		+
		+	[[Category:Tutorials]]
		+	[[Category:Scripting]]

← Older revision	Revision as of 03:49, 28 March 2014
(No difference)

@@ Line 6: / Line 6: @@
 text editor and save it in text format under an arbitrary file name,
 let's say we save it as script.txt in the PyMOL working directory.
 == Python or Pymol? ==
 Then, you have to find out wheter the script you want to run is a