[phenixbb] Ignoring SegIDs
Stephen Graham
stepheng at strubi.ox.ac.uk
Thu Apr 10 05:12:44 PDT 2008
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 <rwgk at cci.lbl.gov> wrote:
> 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 ---------------------------------------
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>
--
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
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