Ccp4 contact - Revision history

Pyadmin: 9 revisions

2014-03-28T01:49:12Z

9 revisions

Dalyte: Authors corrected.

2012-02-13T22:15:26Z

Authors corrected.

Tlinnet at 15:01, 15 January 2012

2012-01-15T15:01:14Z

Tlinnet at 23:19, 13 January 2012

2012-01-13T23:19:35Z

Tlinnet: moved SelectCONTACTContacts to Ccp4 contact: small letters

2011-12-14T19:29:43Z

moved SelectCONTACTContacts to Ccp4 contact: small letters

Tlinnet at 19:28, 14 December 2011

2011-12-14T19:28:24Z

Tlinnet: /* Example 1 */

2011-12-14T19:22:48Z

Example 1

Tlinnet at 19:21, 14 December 2011

2011-12-14T19:21:47Z

Dalyte: Minor fixes

2011-06-20T09:09:51Z

Minor fixes

Dalyte: added a new script to parse and select CONTACT output

2011-06-19T20:34:45Z

added a new script to parse and select CONTACT output

New page

[[File:HhaExample.png|thumb|300px|right|Interface residues (at cutoff <4A) in the 2c7r.pdb were found using NCONT, but similar results can be obtained using this script and CONTACT output. Usage of selectCONTACTContacts script in PyMOL allows easy selection of residues and atoms listed in the output file. Interacting protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.]]

== Overview ==

The script selects residues and atoms from the list of the contacts found by CONTACT from CCP4 Program Suite (CONTACT analyses contacts between subsets of atoms in a PDB file).
First, we run CONTACT on our pdb file to find interface residues. Then by using the selectCONTACTContacts script in PyMOL we separately select residues and atoms listed in a ncont.log file. This generates two selections (atoms and residues) for each interacting chain, allowing quick manipulation of (sometimes) extensive lists in CONTACT log file.

== Usage ==

selectCONTACTContacts( contactsfile, selName1 = "source", selName2 = "target" )

== Examples ==

First use CONTACT to find interface residues/atoms in the pdb file. Once you have ncont.log file proceed to PyMOL.
Make sure you've run the selectCONTACTContacts script first.

fetch 2c7r
selectCONTACTContacts ncont.log, selName1=prot, selName2=dna

[[File:HhaI20example.png|thumb|300px|right|Quick and easy selection of interacting residues and atoms listed in the CONTACT log file. Protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.]]

== The Code ==
<source lang="python">
import re

def parseCONTACTContacts( f ):
# Lys 24A ca Asp 263D CG ... 4.94 [ -1B ] 3: -X, Y+1/2, -Z+1/2
conParser = re.compile("(\S*)\s*(\d+)([A-Z])\s*(\w+)")
s1 = []
s2 = []
for line in f:
if line.startswith('#'):
continue
matches = conParser.findall(line)
if len(matches) == 2:
s1.append(matches[0])
s2.append(matches[1])
elif len(matches) == 1:
s2.append(matches[0])

return (s1, s2)

def selectCONTACTContacts( contactsfile, selName1 = "source", selName2 = "target" ):
"""
selectCONTACTContacts -- parses CCP4/CONTACT log file and selects residues and atoms.
http://www.ccp4.ac.uk/html/contact.html

PARAMS
contactsfile
filename of the CCP4/CONTACT 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
4 selections of interface residues and atoms are created and named
depending on what you passed into selName1 and selName2

REPOSITORY
https://github.com/GerhardR/pymol-scripts

AUTHOR
Gerhard Reitmayr and Dalia Daujotyte, 2011.
"""
# read and parse contacts file into two lists of contact atoms and contact pair list
s1, s2 = parseCONTACTContacts(open(contactsfile))

# create a selection for the first contact list

# create the PYMOL selection macros for the residues
resNames = [chain+"/"+residue+"/" for (type, residue, chain, atom) in s1]
# put them in a set to remove duplicates and then join with 'or'
resSel = " or ".join(frozenset(resNames))
# finally select them under the new name
cmd.select(selName1 + "_res", resSel)

atomNames = [chain+"/"+residue+"/"+atom for (type, residue, chain, atom) in s1]
atomSel = " or ".join(frozenset(atomNames))
cmd.select(selName1 + "_atom", atomSel)

# create a selection for the second contact list

resNames = [chain+"/"+residue+"/" for (type, residue, chain, atom) in s2]
resSel = " or ".join(frozenset(resNames))
cmd.select(selName2 + "_res", resSel)

atomNames = [chain+"/"+residue+"/"+atom for (type, residue, chain, atom) in s2]
atomSel = " or ".join(frozenset(atomNames))
cmd.select(selName2 + "_atom", atomSel)

cmd.extend("selectCONTACTContacts", selectCONTACTContacts)
</source>

== Code repository ==

The latest version of this script and related scripts is available at https://github.com/GerhardR/pymol-scripts.

[[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]]

@@ Line 2: / Line 2: @@
 |type      = script
 |filename  = ccp4_contact.py
-|author    = [[User:Dalyte|Gerhard]]
+|author    = [[User:Dalyte|Gerhard Reitmayr and Dalia Daujotyte]]
 |license   = GPL
 }}

← Older revision		Revision as of 15:01, 15 January 2012
Line 62:		Line 62:
	</syntaxhighlight>		</syntaxhighlight>

−	[[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]]	+	[[Category:Script_Library]]
		+	[[Category:ThirdParty Scripts]]
		+	[[Category:Structural Biology Scripts]]
		+	[[Category:Pymol-script-repo]]

@@ Line 2: / Line 2: @@
 |type      = script
 |filename  = ccp4_contact.py
-|author    = [[Users:Dalyte|Gerhard]]
+|author    = [[User:Dalyte|Gerhard]]
 |license   = GPL
 }}

@@ Line 28: / Line 28: @@
 {{Template:PymolScriptRepoDownload|examples/ccp4_contact_1.pml}}
 <include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/ccp4_contact_1.pml" highlight="python" />
 [[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]]

@@ Line 22: / Line 22: @@
   fetch 2c7r
-  selectCONTACTContacts 2c7r.contact, selName1=prot, selName2=dna
+  ccp4_contact 2c7r.contact, selName1=prot, selName2=dna
 [[File:HhaI20example.png|thumb|300px|right|Quick and easy selection of interacting residues and atoms listed in the CONTACT log file. Protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.]]

← Older revision	Revision as of 01:49, 28 March 2014
(No difference)

← Older revision	Revision as of 19:29, 14 December 2011
(No difference)

@@ Line 1: / Line 1: @@
-[[File:HhaExample.png|thumb|300px|right|Interface residues (at cutoff <4A) in the 2c7r.pdb were found using NCONT, but similar results can be obtained using this script and CONTACT output. Usage of selectCONTACTContacts script in PyMOL allows easy selection of residues and atoms listed in the output file. Interacting protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.]]
+{{Infobox script-repo
 == Overview ==
 The script selects residues and atoms from the list of the contacts found by CONTACT from CCP4 Program Suite (CONTACT analyses contacts between subsets of atoms in a PDB file).
-First, we run CONTACT on our pdb file to find interface residues. Then by using the selectCONTACTContacts script in PyMOL we separately select residues and atoms listed in the output file. This generates two selections (atoms and residues) for each interacting chain, allowing quick manipulation of (sometimes) extensive lists in CONTACT log file.
+First, we run CONTACT on our pdb file to find interface residues. Then by using the ccp4_contact script in PyMOL we separately select residues and atoms listed in the output file. This generates two selections (atoms and residues) for each interacting chain, allowing quick manipulation of (sometimes) extensive lists in CONTACT log file.
 == Usage ==
-selectCONTACTContacts( contactsfile, selName1 = "source", selName2 = "target" )
+ccp4_contact( contactsfile, selName1 = "source", selName2 = "target" )
 First use CONTACT to find interface residues/atoms in the pdb file. Once you have the log file proceed to PyMOL.
-Make sure you've run the selectCONTACTContacts script first.
+Make sure you import the ccp4_contact script first.
   fetch 2c7r
-  selectCONTACTContacts cont.log, selName1=prot, selName2=dna
+  selectCONTACTContacts 2c7r.contact, selName1=prot, selName2=dna
 [[File:HhaI20example.png|thumb|300px|right|Quick and easy selection of interacting residues and atoms listed in the CONTACT log file. Protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.]]
-== The Code ==
+{{Template:PymolScriptRepoDownload|examples/ccp4_contact_1.pml}}
-<source lang="python">
+<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/ccp4_contact_1.pml" highlight="python" />
 [[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]]