Krishan,
Here is a simple stand-alone python script that should do what you want.
Greg
#!/usr/bin/python
#
# rechainpdb.py
# usage:
# python rechainpdb.py mypdbfile1.pdb mypdbfile2.pdb mypdbfile3.pdb
#
# This will generate a new file with all pdbfile (ATOMs and HETATMs) in a single
# file, with each pdbfile having a different chain id. Max pdbs is 26.
#
#ATOM 1 N ASP W 175 24.971 27.228 -12.398 1.00161.17 N
#12345678901234567890123456789012345678901234567890123456789012345678901234567890
# 1 2 3 4 5 6 7 8
#
# chain id is char 22
import sys
if (len(sys.argv)==1):
# no arguments were given
print "+++++++++++++++++++++++++++++++++++++++++++++++++++++++"
print "YOU NEED TO SUPPLY A LIST OF PDB FILES."
print "e.g."
print "python rechainpdb.py mypdbfile1.pdb mypdbfile2.pdb"
print ""
print "This will generate a single new file with each pdb in"
print "the list having a different chain id."
print "+++++++++++++++++++++++++++++++++++++++++++++++++++++++"
sys.exit("\nExiting...\n")
#possible chain ids
CHAINLIST="ABCDEFGHIJKLMNOPQRSTUVWXYZ"
filelist=[]
#OUTPUT file name - default is to use the name of first pdb
outputfilename=sys.argv[1][:-4]+"_allfiles.pdb"
# generate a list of lists, where each file listed after the script
# is a list of strings (lines)
for x in range(1,len(sys.argv)):
currentfile = open(sys.argv[x],'r')
crudefile=currentfile.readlines()
currentfile.close()
cleanfile=[]
for line in crudefile:
cleanfile.append(line.strip())
filelist.append(cleanfile)
# set up output file
outputfile = open(outputfilename,'w')
# write out one large pdbfile with each having a unique chain id
for x in range(0,len(filelist)):
for line in filelist[x]:
if ((line[0:4]=="ATOM") or (line[0:6]=="HETATM")):
print >>outputfile, line[:21]+CHAINLIST[x]+line[22:]
print
print "# # # # # # # # # # # # # # # # # # # # # # #"
print
print "The following chain ids were given to the input pdbfiles:"
print
for i in range(1,len(sys.argv)):
print "chain id given:", CHAINLIST[i-1],sys.argv[i]
print "- - - - - - - - - - - - - - - - - - - - - - - -"
print
print "Final file created:",outputfilename
print
print "# # # # # # # # # # # # # # # # # # # # # # #"
On Apr 8, 2011, at 7:17 AM, krishan wrote:
> Dear CCP4BB members,
> We are using a script written in python to generate symmetry mates for a
> given pdb file using PYMOL. After generating symmetry mates we want to
> combine all the symmetry molecules in a single PDB file with all the chains
> having unique chain IDs. Since all the symmetry mates have same chain ID's I
> was wondering if some one knows a script that can give unique chain ID for
> each symmetry mate. We are interested in script because that dataset that we
> are handling is large.
> I thank you all in advance for your help.
> Best,
>
> Krishan
--
Department of Biophysics
Johns Hopkins University
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3400 N. Charles St.
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Phone: (410) 516-7850 (office)
Phone: (410) 516-3476 (lab)
Fax: (410) 516-4118
gdbow...@jhu.edu
