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Ibrahim M. Moustafa wrote:
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Hi bb,
I wonder if there is a program, server, script that can analyze the
pdb file to enlist the missing residues (for the case in my hand,
REMARK 465 is absent from the pdb file while the structure is full of
gaps!).
I looked in utility programs like moleman2, pdbset, and tried to
google but couldn't find a suitable tool.
thanks,
Ibrahim
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802
Tel (814) 863 8703
Fax (814) 865 7927
You could use the EBI-SSM server http://www.ebi.ac.uk/msd-srv/ssm/ and
run a secondary structure matching. It will try to match the structure
to it's closest know relative and print out a sequence alignment. You
can do this also with other 3d alignment programs e.g. Tcoffee etc.
http://igs-server.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi
You will still have to look at the output but you will quickly see which
parts are missing in your structure.
Jürgen
--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
