Category talk:Script Library - Revision history

Pyadmin: 23 revisions

2014-03-28T01:30:21Z

23 revisions

Tlinnet: /* GitHub for Pymol-scripts */

2011-12-03T09:56:51Z

GitHub for Pymol-scripts

Tlinnet: /* Notes */

2011-12-03T09:56:19Z

Notes

New page

= Requests =
== Introduction ==
Please place your PyMOL script requests here. A few other people might have the same request and someone might just code it up for free (viz. all these other scripts). There are no guarantees that someone will write your script, but it doesn't hurt asking.

'''ExampleScriptTitle'''
:: Example text of what the new awesome script is supposed to do in PyMOL. Consider posting some contact information, so once the script is posted you are apprised.

== List of Requested Scripts ==

'''Dang Reader'''
:: It would be nice if PyMOL could read in and visualize the Dangle (http://kinemage.biochem.duke.edu/software/dangle.php) colon delimited output or be scripted to reproduce the actual data itself for visualization.

==Instruction request==
Would it be possible to add short instructions to category page for new users how to run scripts in pymol...(?)

Maybe this helps: [[Running_Scripts]] (I didn't dare to edit the nice yellow table :-) ) --[[User:Karo|Karo]] 11:19, 5 August 2010 (UTC)

= Policy =
== Rules ==
We want the script library to be as valuable as possible to the public. Therefore, please follow these rules when posting code to the wiki:
* Only post code if you have the legal right to do so
* All posted code must be released under some [http://www.opensource.org/licenses|open source license] or freer (public domain).
** Authors may maintain copyright
** Only post links to code that is not open source licensed, do not copy it onto the wiki

== Depositing Scripts ==
* Create a new page for your script
* Please provide
** an overview of what the script does
** any usage comments or hints
** the source code
* Please add the following to the bottom of your new page:<br><nowiki>[[Category:Script_Library]]
[[Category:PUT_SUBCATEGORY_NAME_HERE]]</nowiki>

= General Notes =
== Notes ==
* Feel free to add scripts (see [[#Rules|rules]] below).
* Feel free to add new categories
* You can make script requests on this page's discussion page
* [https://github.com/Pymol-Scripts/Pymol-script-repo GIT Repository] of all our scripts: <source lang="python">git clone git://github.com/Pymol-Scripts/Pymol-script-repo.git</source>

== GitHub for Pymol-scripts==
I created a github for the pymol scripts. I think this is a good way to to collect and enlarge the collection of scripts. The repo is public accessible so contribute. If you need help on git just write me an email.

http://github.com/jlec/Pymol-script-repo

Karo at 11:19, 5 August 2010

2010-08-05T11:19:16Z

Dalyte at 14:13, 20 November 2009

2009-11-20T14:13:30Z

Dalyte at 14:11, 20 November 2009

2009-11-20T14:11:00Z

Protoconid: /Instruction request/

2009-10-28T15:19:03Z

Instruction request

Erbseah at 15:17, 14 August 2009

2009-08-14T15:17:06Z

New page

= Requests =
Please place your PyMOL script requests here. A few other people might have the same request and someone might just code it up for free (viz. all these other scripts). There are no guarantees that someone will write your script, but it doesn't hurt asking.

'''ExampleScriptTitle'''
:: Example text of what the new awesome script is supposed to do in PyMOL. Consider posting some contact information, so once the script is posted you are apprised.

= Policy =
== Rules ==
We want the script library to be as valuable as possible to the public. Therefore, please follow these rules when posting code to the wiki:
* Only post code if you have the legal right to do so
* All posted code must be released under some [http://www.opensource.org/licenses|open source license] or freer (public domain).
** Authors may maintain copyright
** Only post links to code that is not open source licensed, do not copy it onto the wiki

== Depositing Scripts ==
* Create a new page for your script
* Please provide
** an overview of what the script does
** any usage comments or hints
** the source code
* Please add the following to the bottom of your new page:<br><nowiki>[[Category:Script_Library]]
[[Category:PUT_SUBCATEGORY_NAME_HERE]]</nowiki>

= General Notes =
== Notes ==
* Feel free to add scripts (see [[#Rules|rules]] below).
* Feel free to add new categories
* You can make script requests on this page's discussion page
* [http://github.com/jlec/Pymol-script-repo GIT Repository] of all our scripts: <source lang="python">git clone git://github.com/jlec/Pymol-script-repo.git</source>

== GitHub for Pymol-scripts==
I created a github for the pymol scripts. I think this is a good way to to collect and enlarge the collection of scripts. The repo is public accessible so contribute. If you need help on git just write me an email.

http://github.com/jlec/Pymol-script-repo

Erbseah: /* Requests */

2009-08-13T21:38:43Z

Requests

New page

= Requests =
Please place your PyMOL script requests here. A few other people might have the same request and someone might just code it up for free (viz. all these other scripts). There are no guarantees that someone will write your script, but it doesn't hurt asking.

'''ExampleScriptTitle'''
:: Example text of what the new awesome script is supposed to do in PyMOL. Consider posting some contact information, so once the script is posted you are apprised.

'''Get xyz coordinates'''

I am looking for a way to get coorinates for all the atom in a residue after I have modified it.

= Policy =
== Rules ==
We want the script library to be as valuable as possible to the public. Therefore, please follow these rules when posting code to the wiki:
* Only post code if you have the legal right to do so
* All posted code must be released under some [http://www.opensource.org/licenses|open source license] or freer (public domain).
** Authors may maintain copyright
** Only post links to code that is not open source licensed, do not copy it onto the wiki

== Depositing Scripts ==
* Create a new page for your script
* Please provide
** an overview of what the script does
** any usage comments or hints
** the source code
* Please add the following to the bottom of your new page:<br><nowiki>[[Category:Script_Library]]
[[Category:PUT_SUBCATEGORY_NAME_HERE]]</nowiki>

= General Notes =
== Notes ==
* Feel free to add scripts (see [[#Rules|rules]] below).
* Feel free to add new categories
* You can make script requests on this page's discussion page
* [http://github.com/jlec/Pymol-script-repo GIT Repository] of all our scripts: <source lang="python">git clone git://github.com/jlec/Pymol-script-repo.git</source>

== GitHub for Pymol-scripts==
I created a github for the pymol scripts. I think this is a good way to to collect and enlarge the collection of scripts. The repo is public accessible so contribute. If you need help on git just write me an email.

http://github.com/jlec/Pymol-script-repo

Jlec at 10:10, 1 May 2009

2009-05-01T10:10:03Z

New page

== GitHub for Pymol-scripts==
I created a github for the pymol scripts. I think this is a good way to to collect and enlarge the collection of scripts. The repo is public accessible so contribute. If you need help on git just write me an email.

http://github.com/jlec/Pymol-script-repo

About the rasmolify script, there's a project to translate between the languages [http://arcib.dowling.edu/sbevsl/].
It's in pre-alpha, apparently, but this kind of language translation seems like a tricky problem. It's on my list of things to do...--[[User:Gilleain|Gilleain]] 19:27, 18 February 2008 (CST)

: To be honest I was thinking of a quick hack rather than anything fancy. Thanks very much for the pointer though! --[[User:Dan|Dan]] 02:45, 19 February 2008 (CST)

== Depositing Scripts ==
* Create a new page for your script
* Please provide
** an overview of what the script does
** any usage comments or hints
** the source code
* Please add the following to the bottom of your new page:<br><nowiki>[[Category:Script_Library]]
[[Category:PUT_SUBCATEGORY_NAME_HERE]]</nowiki>

== Feedback on Changes ==

Please let me know if you like the new changes.

← Older revision		Revision as of 09:56, 3 December 2011
Line 45:		Line 45:
	I created a github for the pymol scripts. I think this is a good way to to collect and enlarge the collection of scripts. The repo is public accessible so contribute. If you need help on git just write me an email.		I created a github for the pymol scripts. I think this is a good way to to collect and enlarge the collection of scripts. The repo is public accessible so contribute. If you need help on git just write me an email.

−	~~http~~://github.com/~~jlec~~/Pymol-script-repo	+	https://github.com/Pymol-Scripts/Pymol-script-repo

← Older revision		Revision as of 14:13, 20 November 2009
Line 38:		Line 38:

	http://github.com/jlec/Pymol-script-repo		http://github.com/jlec/Pymol-script-repo
−
−	~~== ContactsNCONT ==~~
−
−	~~[[File:HhaExample.png]]~~
−
−	~~Interface residues (at cutoff <4A) in the 2c7r.pdb were found using NCONT. Usage of ContactsNCONT script in PyMOL allows easy~~
−	~~selection of residues and atoms listed in ncont.log file. Interacting protein and DNA residues are colored in red and slate,~~
−	~~respectively. Atoms in contact are in dots.~~
−
−	~~== Overview ==~~
−
−	~~The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite (NCONT analyses contacts between subsets of atoms in a PDB file).~~
−	First, we run NCONT on our pdb file to find interface residues. Then by using the ContactsNCONT script in PyMOL we select listed residues and atoms separately. This generates two selections (atoms and residues) for each interacting chain, allowing quick manipulation of (sometimes) extensive lists in NCONT log file.
−
−
−	~~== Usage ==~~
−
−	~~selectContacts( contactsfile, selName1 = "source", selName2 = "target" )~~
−
−
−	~~== Examples ==~~
−
−
−	~~''First use NCONT to find interface residues/atoms in the same pdb file. Once you have ncont.log file proceed to PyMOL.''~~
−	~~''Make sure you've run the ContactsNCONT script first.''~~
−
−	~~fetch 2c7r~~
−	~~selectContacts ncont.log, selName1=prot, selName2=dna~~
−
−
−	~~== The Code ==~~
−
−
−	~~import re~~
−
−	~~def parseContacts( f ):~~
−	~~# /1/B/ 282(PHE). / CE1[ C]: /1/E/ 706(GLN). / O [ O]: 3.32~~
−	~~conParser = re.compile("\s/(\d+)/([A-Z])/\s(\d+).?/\s([A-Z0-9]).?:")~~
−	~~mode = 0~~
−	~~s1 = []~~
−	~~s2 = []~~
−	~~pairs = []~~
−	~~for line in f:~~
−	~~if mode == 0:~~
−	~~if line.strip().startswith("SOURCE ATOMS"):~~
−	~~mode = 1~~
−	~~elif mode == 1:~~
−	~~mode = 2~~
−	~~elif mode == 2:~~
−	~~matches = conParser.findall(line)~~
−	~~if len(matches) == 0:~~
−	~~return (s1, s2, pairs)~~
−	~~if len(matches) == 2:~~
−	~~s1.append(matches[0])~~
−	~~s2.append(matches[1])~~
−	~~elif len(matches) == 1:~~
−	~~s2.append(matches[0])~~
−	~~pairs.append((len(s1)-1, len(s2)-1))~~
−	~~else:~~
−	~~print "Unknown mode", mode~~
−
−	~~def selectContacts( contactsfile, selName1 = "source", selName2 = "target" ):~~
−	~~"""~~
−	~~selectContacts -- parses CCP4 NCONT log file and selects residues and atoms from the list of the contacts found.~~
−
−	~~PARAMS~~
−	~~contactsfile~~
−	~~filename of the CCP4 NCONT contacts log file~~
−
−	~~selName1~~
−	~~the name prefix for the _res and _atom selections returned for the~~
−	~~source set of chain~~
−
−	~~selName2~~
−	~~the name prefix for the _res and _atom selections returned for the~~
−	~~target set of chain~~
−
−	~~RETURNS~~
−	* 2 selections of interface residues and atoms for each chain are created and named
−	~~depending on what you passed into selName1 and selName2~~
−
−	~~AUTHOR:~~
−	~~Gerhard Reitmayr and Dalia Daujotyte, 2009.~~
−	~~"""~~
−	~~# read and parse contacts file into two lists of contact atoms and contact pair list~~
−	~~s1, s2, pairs = parseContacts(open(contactsfile))~~
−	~~# create a selection for the first contact list~~
−	~~resName = selName1 + "_res"~~
−	~~atomName = selName1 + "_atom"~~
−	~~cmd.select(resName, None)~~
−	~~cmd.select(atomName, None)~~
−	~~for (thing, chain, residue, atom) in s1:~~
−	~~cmd.select( resName, resName + " or " + chain+"/"+residue+"/")~~
−	~~cmd.select( atomName, atomName + " or " + chain+"/"+residue+"/"+atom)~~
−
−	~~# create a selection for the second contact list~~
−	~~resName = selName2 + "_res"~~
−	~~atomName = selName2 + "_atom"~~
−	~~cmd.select(resName, None)~~
−	~~cmd.select(atomName, None)~~
−	~~for (thing, chain, residue, atom) in s2:~~
−	~~cmd.select( resName, resName + " or " + chain+"/"+residue+"/")~~
−	~~cmd.select( atomName, atomName + " or " + chain+"/"+residue+"/"+atom)~~
−
−	~~cmd.extend("selectContacts", selectContacts)~~
−
−
−	~~[[Category:Script_Library]] [[Category:Third Party]] [[Category:Structural Biology]]~~

← Older revision		Revision as of 14:11, 20 November 2009
Line 38:		Line 38:

	http://github.com/jlec/Pymol-script-repo		http://github.com/jlec/Pymol-script-repo
		+
		+	== ContactsNCONT ==
		+
		+	[[File:HhaExample.png]]
		+
		+	Interface residues (at cutoff <4A) in the 2c7r.pdb were found using NCONT. Usage of ContactsNCONT script in PyMOL allows easy
		+	selection of residues and atoms listed in ncont.log file. Interacting protein and DNA residues are colored in red and slate,
		+	respectively. Atoms in contact are in dots.
		+
		+	== Overview ==
		+
		+	The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite (NCONT analyses contacts between subsets of atoms in a PDB file).
		+	First, we run NCONT on our pdb file to find interface residues. Then by using the ContactsNCONT script in PyMOL we select listed residues and atoms separately. This generates two selections (atoms and residues) for each interacting chain, allowing quick manipulation of (sometimes) extensive lists in NCONT log file.
		+
		+
		+	== Usage ==
		+
		+	selectContacts( contactsfile, selName1 = "source", selName2 = "target" )
		+
		+
		+	== Examples ==
		+
		+
		+	''First use NCONT to find interface residues/atoms in the same pdb file. Once you have ncont.log file proceed to PyMOL.''
		+	''Make sure you've run the ContactsNCONT script first.''
		+
		+	fetch 2c7r
		+	selectContacts ncont.log, selName1=prot, selName2=dna
		+
		+
		+	== The Code ==
		+
		+
		+	import re
		+
		+	def parseContacts( f ):
		+	# /1/B/ 282(PHE). / CE1[ C]: /1/E/ 706(GLN). / O [ O]: 3.32
		+	conParser = re.compile("\s/(\d+)/([A-Z])/\s(\d+).?/\s([A-Z0-9]).?:")
		+	mode = 0
		+	s1 = []
		+	s2 = []
		+	pairs = []
		+	for line in f:
		+	if mode == 0:
		+	if line.strip().startswith("SOURCE ATOMS"):
		+	mode = 1
		+	elif mode == 1:
		+	mode = 2
		+	elif mode == 2:
		+	matches = conParser.findall(line)
		+	if len(matches) == 0:
		+	return (s1, s2, pairs)
		+	if len(matches) == 2:
		+	s1.append(matches[0])
		+	s2.append(matches[1])
		+	elif len(matches) == 1:
		+	s2.append(matches[0])
		+	pairs.append((len(s1)-1, len(s2)-1))
		+	else:
		+	print "Unknown mode", mode
		+
		+	def selectContacts( contactsfile, selName1 = "source", selName2 = "target" ):
		+	"""
		+	selectContacts -- parses CCP4 NCONT log file and selects residues and atoms from the list of the contacts found.
		+
		+	PARAMS
		+	contactsfile
		+	filename of the CCP4 NCONT contacts log file
		+
		+	selName1
		+	the name prefix for the _res and _atom selections returned for the
		+	source set of chain
		+
		+	selName2
		+	the name prefix for the _res and _atom selections returned for the
		+	target set of chain
		+
		+	RETURNS
		+	* 2 selections of interface residues and atoms for each chain are created and named
		+	depending on what you passed into selName1 and selName2
		+
		+	AUTHOR:
		+	Gerhard Reitmayr and Dalia Daujotyte, 2009.
		+	"""
		+	# read and parse contacts file into two lists of contact atoms and contact pair list
		+	s1, s2, pairs = parseContacts(open(contactsfile))
		+	# create a selection for the first contact list
		+	resName = selName1 + "_res"
		+	atomName = selName1 + "_atom"
		+	cmd.select(resName, None)
		+	cmd.select(atomName, None)
		+	for (thing, chain, residue, atom) in s1:
		+	cmd.select( resName, resName + " or " + chain+"/"+residue+"/")
		+	cmd.select( atomName, atomName + " or " + chain+"/"+residue+"/"+atom)
		+
		+	# create a selection for the second contact list
		+	resName = selName2 + "_res"
		+	atomName = selName2 + "_atom"
		+	cmd.select(resName, None)
		+	cmd.select(atomName, None)
		+	for (thing, chain, residue, atom) in s2:
		+	cmd.select( resName, resName + " or " + chain+"/"+residue+"/")
		+	cmd.select( atomName, atomName + " or " + chain+"/"+residue+"/"+atom)
		+
		+	cmd.extend("selectContacts", selectContacts)
		+
		+
		+	[[Category:Script_Library]] [[Category:Third Party]] [[Category:Structural Biology]]

← Older revision	Revision as of 01:30, 28 March 2014
(No difference)

@@ Line 8: / Line 8: @@
 ==Instruction request==
 Would it be possible to add short instructions to category page for new users how to run scripts in pymol...(?)
 = Policy =

← Older revision		Revision as of 15:19, 28 October 2009
Line 5:		Line 5:
	:: Example text of what the new awesome script is supposed to do in PyMOL. Consider posting some contact information, so once the script is posted you are apprised.		:: Example text of what the new awesome script is supposed to do in PyMOL. Consider posting some contact information, so once the script is posted you are apprised.

		+
		+	==Instruction request==
		+	Would it be possible to add short instructions to category page for new users how to run scripts in pymol...(?)

	= Policy =		= Policy =

Category talk:Script Library - Revision history

Pyadmin: 23 revisions

Tlinnet: /* GitHub for Pymol-scripts */

Tlinnet: /* Notes */

Karo at 11:19, 5 August 2010

Dalyte at 14:13, 20 November 2009

Dalyte at 14:11, 20 November 2009

Protoconid: /*Instruction request*/

Erbseah at 15:17, 14 August 2009

Erbseah: /* Requests */

Jlec at 10:10, 1 May 2009

Protoconid: /Instruction request/