Pyadmin: 18 revisions

2014-03-28T01:06:36Z

18 revisions

Dalyte: Authors corrected.

2012-02-13T22:16:29Z

Authors corrected.

Tlinnet: /* Use of NCONT - for Linux */

2012-01-15T15:01:35Z

Use of NCONT - for Linux

Tlinnet at 23:21, 13 January 2012

2012-01-13T23:21:09Z

Tlinnet: moved SelectNCONTContacts to Ccp4 ncont: small letters

2011-12-14T20:35:27Z

moved SelectNCONTContacts to Ccp4 ncont: small letters

Tlinnet at 20:34, 14 December 2011

2011-12-14T20:34:45Z

Show changes

Dalyte: fixed long comment

2011-06-19T20:21:43Z

fixed long comment

Dalyte: updated script with faster selection and naming scheme.

2011-06-19T20:19:12Z

updated script with faster selection and naming scheme.

Dalyte: moved ContactsNCONT to SelectNCONTContacts: unify naming scheme for new scripts

2011-06-19T20:14:06Z

moved ContactsNCONT to SelectNCONTContacts: unify naming scheme for new scripts

Mglerner: /* The Code */

2011-05-26T13:49:00Z

The Code

@@ Line 2: / Line 2: @@
 |type      = script
 |filename  = ccp4_ncont.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 69:		Line 69:


−	[[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_ncont.py
-|author    = [[Users:Dalyte|Gerhard]]
+|author    = [[User:Dalyte|Gerhard]]
 |license   = GPL
 }}

@@ Line 30: / Line 30: @@
 def parseNCONTContacts( 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]*).*?:") # * in the second group is needed when chain code is blank
+    # * in the second group is needed when chain code is blank
      mode = 0
      s1 = []

@@ Line 1: / Line 1: @@
-[[File:HhaExample.png|thumb|300px|right|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 shown in dots.]]
+[[File:HhaExample.png|thumb|300px|right|Interface residues (at cutoff <4A) in the 2c7r.pdb were found using NCONT. Usage of selectNCONTContacts 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 shown 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 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 NCONT log file.
+First, we run NCONT on our pdb file to find interface residues. Then by using the selectNCONTContacts 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 NCONT log file.
 This script works best for intermolecular contacts (when NCONT target and source selections don't overlap). If crystal contacts (NCONT parameter cell = 1 or 2) are included then additional coding is required to distinguish inter from intramolecular contacts.
@@ Line 10: / Line 10: @@
 == Usage ==
-selectContacts( contactsfile, selName1 = "source", selName2 = "target" )
+selectNCONTContacts( contactsfile, selName1 = "source", selName2 = "target" )
@@ Line 17: / Line 17: @@
 First use NCONT to find interface residues/atoms in the pdb file. Once you have ncont.log file proceed to PyMOL.
-Make sure you've run the ContactsNCONT script first.
+Make sure you've run the selectNCONTContacts script first.
   fetch 2c7r
-  selectContacts ncont.log, selName1=prot, selName2=dna
+  selectNCONTContacts ncont.log, selName1=prot, selName2=dna
 [[File:HhaI20example.png|thumb|300px|right|Quick and easy selection of interacting residues and atoms listed in the NCONT log file. Protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.]]
@@ Line 27: / Line 27: @@
 <source lang="python">
 import re
-−
-def parseContacts( f ):
+def parseNCONTContacts( 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]*).*?:")
+     conParser = re.compile("\s*/(\d+)/([A-Z]*)/\s*(\d+).*?/\s*([A-Z0-9]*).*?:") # * in the second group is needed when chain code is blank
      mode = 0
      s1 = []
@@ Line 54: / Line 53: @@
          else:
              print "Unknown mode", mode
-−
-def selectContacts( contactsfile, selName1 = "source", selName2 = "target" ):
+def selectNCONTContacts( contactsfile, selName1 = "source", selName2 = "target" ):
      """
-     selectContacts -- parses CCP4 NCONT log file and selects residues and atoms from the list of the contacts found.
+     selectContacts -- parses CCP4/NCONT log file and selects residues and atoms.
+    http://www.ccp4.ac.uk/html/ncont.html
      PARAMS
          contactsfile
-             filename of the CCP4 NCONT contacts log file
+             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
+selections of interface residues and atoms are created and named
-            depending on what you passed into selName1 and selName2
+        depending on what you passed into selName1 and selName2
-−
-     AUTHOR:
+    REPOSITORY
-         Gerhard Reitmayr and Dalia Daujotyte, 2009.
+        https://github.com/GerhardR/pymol-scripts
      """
      # read and parse contacts file into two lists of contact atoms and contact pair list
-     s1, s2, pairs = parseContacts(open(contactsfile))
+     s1, s2, pairs = parseNCONTContacts(open(contactsfile))
      # create a selection for the first contact list
-     resName = selName1 + "_res"
-     atomName = selName1 + "_atom"
+    # create the PYMOL selection macros for the residues
-     cmd.select(resName, None)
+    resNames = [chain+"/"+residue+"/" for (type, chain, residue, atom) in s1]
-     cmd.select(atomName, None)
+     # put them in a set to remove duplicates and then join with 'or'
-     for (thing, chain, residue, atom) in s1:
+    resSel = " or ".join(frozenset(resNames))
-        cmd.select( resName, resName + " or " + chain+"/"+residue+"/")
+     # finally select them under the new name
-        cmd.select( atomName, atomName + " or " + chain+"/"+residue+"/"+atom)
+     cmd.select(selName1 + "_res", resSel)
-−
      # create a selection for the second contact list
-     resName = selName2 + "_res"
-     atomName = selName2 + "_atom"
+     resNames = [chain+"/"+residue+"/" for (type, chain, residue, atom) in s2]
-    cmd.select(resName, None)
+     resSel = " or ".join(frozenset(resNames))
-     cmd.select(atomName, None)
+     cmd.select(selName2 + "_res", resSel)
-     for (thing, chain, residue, atom) in s2:
-        cmd.select( resName, resName + " or " + chain+"/"+residue+"/")
+    atomNames = [chain+"/"+residue+"/"+atom for (type, chain, residue, atom) in s2]
-        cmd.select( atomName, atomName + " or " + chain+"/"+residue+"/"+atom)
+    atomSel = " or ".join(frozenset(atomNames))
+    cmd.select(selName2 + "_atom", atomSel)
-cmd.extend("selectContacts", selectContacts)
 </source>
 [[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]]

← Older revision	Revision as of 01:06, 28 March 2014
(No difference)

← Older revision	Revision as of 20:35, 14 December 2011
(No difference)

← Older revision	Revision as of 20:14, 19 June 2011
(No difference)

Ccp4 ncont - Revision history