RE: Helix kink

["Andrej Sali" <Sali AT rockefeller.edu>]

Don't trust modeller ;-) 

You could try to impose ideal helix restraints on the helix and see if
that straightens it.

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 sali AT rockefeller.edu; http://salilab.org

-----Original Message-----
From: owner-modeller_usage@listsrv.ucsf.edu
[mailto:owner-modeller_usage@listsrv.ucsf.edu] On Behalf Of Dan
Thomas Major
Sent: Saturday, January 26, 2002 11:40 AM
To: modeller_usage@listsrv.ucsf.edu
Subject: Helix kink


Hi,
In my template protein there is a proline in a helix that causes a kink
in the helix. This proline residue does not occur in the target
protein,but modeller predicts a kink in the target protein as well.
Should I "trust" modeller that there is likely to be a kink or is there
a way of dealing with this... Thanks, Dan