Coot:
Extension -> Modelling -> Residues with Missing Atoms...
Or watch out for the blue bars in the rotamer validation graph in Coot.
B
Dear all,
Does anyone know a program that will check a PDB file for missing
atoms and output a list of the corresponding residues?
Many thanks in advanc
PDB file for missing atoms
Dear all,
Does anyone know a program that will check a PDB file for missing atoms and
output a list of the corresponding residues?
Many thanks in advance,
Tiago
***
Tiago Barros, PhD
Kuriyan lab
According to the PDB Format document, entries with missing
atoms should have a parsable REMARK 470. You might want
to write some quick code to look for that REMARK.
The PDB staff could comment about the accuracy of REMARK
470 in its entries.
Frances Bernstein
===
Hi Ed,
On Tue, Aug 23, 2011 at 12:39 PM, Ed Pozharski wrote:
> I would be pretty sure there is something like
> phinix.which_atoms_are_missing or such :)
>
good idea! I can turn the script that I just sent into this command so it is
available in a couple of days -:)
Pavel.
Hi Tiago,
easy, two steps:
1) Save the lines between *** into a file say called run.py:
***
import os,sys
from mmtbx.monomer_library import pdb_interpretation
from mmtbx import monomer_library
import mmtbx.monomer_library.server
from cStringIO import StringIO
def exercise(args):
file_name = a
On Tue, 2011-08-23 at 12:19 -0700, Tiago Barros wrote:
> Does anyone know a program that will check a PDB file for missing
> atoms and output a list of the corresponding residues?
REFMAC reports a (truncated?) list in the log file. Coot can also
identify missing atoms. I would be pretty sure th
Dear all,
Does anyone know a program that will check a PDB file for missing atoms and
output a list of the corresponding residues?
Many thanks in advance,
Tiago
***
Tiago Barros, PhD
Kuriyan lab - Molecular and Cellular Biolo
