pymol-users

Re: [PyMOL] Renumber Script problem

[Jordan W. <jwi...@gm...>]

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 <at...@bu...> 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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Re: [PyMOL] Renumber Script problem

[Thomas H. <tho...@sc...>]

Hi Jordan,

nice script, but it does not do the same like the renumber script from
the PyMOLWiki (http://pymolwiki.org/index.php/Renumber). Try this: set
all residue numbers to 1, the renumber script will not care because it
walks along the bonds and increases the count whenever it passes a
peptide bond. The Biopython parser however will read just one residue.

Cheers,
  Thomas

Jordan Willis wrote, On 01/21/13 19:53:
> 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()

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor