Hi all, Apologies if this is a dumb question, but... Is there a way to get phenix.refine to ignore segids? I ask because COOT seems to be blithely unaware of segids and they have a habit of disappearing when one is rebuilding a model, resulting in very odd geometries when the side chain of a residue is in segment ' ' and the main chain is in segment 'A'. Alternatively, is there a 'convert chain IDs to segids' option like in CNS? Basically, I would like the segids removed/fixed/ignored automagically at the start of refinement (since I never use them for anything useful anyway). Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
Hi Stephen, We are addressing this problem for the next release. With the current release, the best approach is to blank out the segid columns, for example with the small script below. Ralf Usage: phenix.python blank_out_segid.py original.pdb > modified.pdb ---------------------------------- cut --------------------------------------- import sys def run(args): for file_name in args: for line in open(file_name).read().splitlines(): if ( line.startswith("ATOM") or line.startswith("HETATM")): line += " " * max(0, 80-len(line)) line = line[:72] + " " + line[76:] print line.rstrip() if (__name__ == "__main__"): run(sys.argv[1:]) ---------------------------------- cut ---------------------------------------
Thanks, that works well.
I'm not sure if it is necessary, but I modified the script to get rid
of segIDs in ANISOU cards too as follows:
---------------------------------- cut ---------------------------------------
import sys
def run(args):
for file_name in args:
for line in open(file_name).read().splitlines():
if ( line.startswith("ATOM")
or line.startswith("HETATM")
or line.startswith("ANISOU")):
line += " " * max(0, 80-len(line))
line = line[:72] + " " + line[76:]
print line.rstrip()
if (__name__ == "__main__"):
run(sys.argv[1:])
---------------------------------- cut ---------------------------------------
Cheers,
Stephen
On 4/9/08, Ralf W. Grosse-Kunstleve
Hi Stephen, We are addressing this problem for the next release. With the current release, the best approach is to blank out the segid columns, for example with the small script below. Ralf
Usage: phenix.python blank_out_segid.py original.pdb > modified.pdb
---------------------------------- cut --------------------------------------- import sys
def run(args): for file_name in args: for line in open(file_name).read().splitlines(): if ( line.startswith("ATOM") or line.startswith("HETATM")): line += " " * max(0, 80-len(line)) line = line[:72] + " " + line[76:] print line.rstrip()
if (__name__ == "__main__"): run(sys.argv[1:]) ---------------------------------- cut --------------------------------------- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549
I'm not sure if it is necessary, but I modified the script to get rid of segIDs in ANISOU cards too as follows:
Yes that makes sense. ... there are also SIGATM card. But hopefully we won't need the script much longer. In my development version the segid columns with gaps are ignored automatically. Thanks! Ralf
There is potentially a worse problem from Coot (which I imagine Paul will fix sometime RSN) where you can end up with ChainID & SEGID different (from the Apply NCS loop command) Phil On 10 Apr 2008, at 17:27, Ralf W. Grosse-Kunstleve wrote:
I'm not sure if it is necessary, but I modified the script to get rid of segIDs in ANISOU cards too as follows:
Yes that makes sense. ... there are also SIGATM card. But hopefully we won't need the script much longer. In my development version the segid columns with gaps are ignored automatically. Thanks! Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
There is potentially a worse problem from Coot (which I imagine Paul will fix sometime RSN) where you can end up with ChainID & SEGID different (from the Apply NCS loop command)
I hope my current algorithm handles this gracefully. But only when it is out in the wild will we know for sure... Ralf
participants (3)
-
PhilEvans -
Ralf W. Grosse-Kunstleve -
Stephen Graham