ContactsNCONT
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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.
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.
Usage
selectContacts( contactsfile, selName1 = "source", selName2 = "target" )
Examples
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.
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]*).*?:") conParser = re.compile("\s*/(\d+)/([A-Z]*)/\s*(\d+).*?/\s*([A-Z0-9]*).*?:") # * is needed when chain code is blank 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)
