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
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
Hi Alex,
the renumber script only sets the residue number, it does not reorder
atoms internally. Just type
PyMOL sort
to sort internally based on the new residue numbers.
See also:
http://pymolwiki.org/index.php/Sort
Cheers,
Thomas
Alex Truong wrote, On 01/21/13 19:21:
Hi All,
I've
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
