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RE: disulfides

It should not be a problem. Would you please send me your input top,
alignment, and atom files. Thanks, Andrej

Andrej Sali, Associate Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail ; http://salilab.org

-----Original Message-----
[">mailto:] On Behalf Of Daniel
John Rigden
Sent: Wednesday, January 23, 2002 7:57 AM
To: Modeller Usage List
Subject: disulfides


Is there a problem with automatic disulfides in Modeller 6?  My recent
models are being produced without the disulfides present in the
templates and I don't remember this being a problem with earlier
versions.  In the log file there is a call to the relevant patch routine

TOP_________>   151  465 PATCH_SS_TEMPLATES

but it doesn't seem to work.  The template files have been processed so
that they have lost PDB headers but I assume MODELLER figures SS bonds
for itself rather than reading SSBOND lines in PDB headers...

We can always define the disulfides manually with the general PATCH
command but, as the manual says, they'll be better defined by
PATCH_SS_TEMPLATES - generated restraints.

Thanks for your help.


|                       Dr Daniel John Rigden
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