thanks for all replies, summarized below:
the suggestion from Gerard did the job. In the entry from S2C
database the missing residues are flagged with "367", you still need
to go through the file; but it is easy to pick the missing parts!
I haven't checked the SSM or TCOFFEE suggestion; but I guess it
should work as well. Procheck reported "Chain Break" in the logfile
but this does not give location of the missing residues; rather it
showed a chain break between "unknown amino acids"
Gerard DVD:
see dunbrack's S2C (database and server) at http://dunbrack.fccc.edu/Guoli/s2c/
Jurgen:
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.
Todd Green,
you can run procheck from ccp4i. it will give you info such as in the log file:
Chain break between 166 (A 169 ) and 167 (A 177 )
which i believe translates to renumbered residue # for last residue
before the break(chain and original res #ing) and renumbered residue
# for first residue after the break(chain and original res #ing)
Thanks Gerard, jurgen and Todd.
regards,
Ibrahim
At 12:25 PM 1/16/2007, you 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
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
