Hi, Since it's a lot easier to do things in Chimera when a file has chain IDs, Maximilian Andrews wrote a script (below) for adding chain IDs to files that lack them. It does require that TER cards be present at the end of chains, but those are a lot easier to add than chain IDs. Enjoy! Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu #! /usr/bin/env python # Filename: rename_pdb_for_chimera.py ###################################################################### # # # Created: Maximilian N. Andrews, July 18, 2005 # # Ciamician, Bologna University # # # # Function: # # # # This script adds a chain ID to all the subunits (column 22) in # # the PDB file. # # The chains are named 'A','B','C',etc. until all of the subunits # # have been labeled. # # # # For the subunits to be renamed properly the PDB must contain a # # line beginning with TER after each subunit, for example: # # ... # # ATOM 1570 OXT HIE 103 24.590 -9.249 30.054 # # TER # # ATOM 1571 N SER 104 16.936 7.767 30.236 # # ... # # # # Notes: # # # # The original file is first read by the script, then copied to a # # backup file - with the same name, but with "~" added at the end # # of it - and then it is renamed and saved with the original name. # # # # Usage: # # # # rename_pdb.py arg1 arg2 # # arg1 is the the number of chains that have to be renamed; # # arg2 is the name of the input file; # # example: rename_pdb.py 4 MY_PDB.pdb # # # ###################################################################### import sys import os def BAILING_OUT(N_ARG): """ The srcipt needs two arguments: [int] The number of subunits to be renamed; [str] The name of the PDB file to be renamed. The correct use of this script is: rename_pdb.py arg1 arg2 arg1 is the number of chains in the protein; arg2 is the name of the input file; example: rename_pdb.py 4 MY_PDB.pdb """ if N_ARG != 3: print BAILING_OUT.__doc__ sys.exit() else: return BAILING_OUT(len(sys.argv)) NUMBER_CHAINS = sys.argv[1] PDB_IN = sys.argv[2] print 'Number of chains is: ',sys.argv[1] print 'The PDB file to rename is: ',sys.argv[2] PDB_OUT = PDB_IN PDB_BAK = PDB_IN+'~' f = open(PDB_IN,'r') lines = f.readlines() f.close() print 'Making backup file '+PDB_BAK+'...' os.rename(PDB_IN,PDB_BAK) print '...done!' print 'Renaming '+PDB_IN+'...' CHAIN = 65 # this is the integer that corrisponds to the character "A" MAX_CHAIN = int(NUMBER_CHAINS) + CHAIN LETTER = chr(CHAIN) NEW_PDB = [] for i in range(len(lines)): line = lines[i] if line.startswith('TER'): CHAIN = CHAIN + 1 if CHAIN < MAX_CHAIN: LETTER = chr(CHAIN) else: LETTER = ' ' if line.startswith('ATOM'): newline=line[0:21]+LETTER+line[22:] NEW_PDB.append(newline) elif line.startswith('TER') and len(line) > 21: # just in case there's a chain identifier in the "TER" line... (the condition len (line) is added just in case the TER line is a just few characters long... i.e. it would add a blank space at the start of the following line) newline=line[0:21]+' '+line[22:] NEW_PDB.append(newline) else: # if line doesn't start with either ATOM or TER, it will print it as is NEW_PDB.append(line) print '...done!' print 'Writing renamed file '+PDB_OUT+'...' f = open(PDB_OUT,'w') for i in range(len(NEW_PDB)): f.write(NEW_PDB[i]) f.close() print '...done!'