Does it have to be a pymol script. Renumbering pdbs is the bread and butter of
biopython pdb module:
#!/blue/meilerlab/apps/Linux2/x86_64/bin/python2.5
import sys
from Bio.PDB import *
from optparse import OptionParser
import warnings
def main():
usage = "%prog input.pdb output.pdb"
parser= OptionParser(usage)
parser.add_option("-n",dest="start",help="residue number to start with,
default is 1",default=1)
parser.add_option("--preserve",dest="preserve",help="preserve insertion
code and heteroflags",default=False, action="store_true")
parser.add_option("--norestart",dest="norestart",help="don't start
renumbering at each chain, default=False",default=False, action="store_true")
(options, args) = parser.parse_args()
warnings.simplefilter('ignore',PDBExceptions.PDBConstructionWarning)
PDBparse = PDBParser(PERMISSIVE=1)
struct = PDBparse.get_structure(args[0][0:3],args[0])
residue_id = int(options.start)
chain_id = ""
for residue in struct.get_residues():
chain = residue.get_parent()
if(chain_id != chain.get_id() and not options.norestart):
chain_id = chain.get_id()
residue_id=int(options.start)
if(options.preserve):
hetero = residue.id[0]
insert = residue.id[2]
residue.id=(hetero,residue_id,insert)
else:
residue.id=(' ',residue_id,' ')
residue_id +=1
io=PDBIO()
io.set_structure(struct)
io.save(args[1])
if __name__ == "__main__":
main()
Jordan
On Jan 21, 2013, at 12:21 PM, Alex Truong <atru...@bu.edu> wrote:
> Hi All,
>
> I've been having a bit of trouble recently with the renumber script. I have a
> pdb file that I'm trying to renumber, but unlike the other times I've used
> it, it is renumbering incorrectly. The numbers are usually spaced out 5
> residues apart, but I have one number right near the beginning that is 6
> residues down from the previous one. Needless to say, this is screwing up the
> rest of the count. Is there any idea why? I've provided a screenshot.
>
> Thanks,
> Alex
> <renumbererror.png>------------------------------------------------------------------------------
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