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
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@rockefeller.edu; http://salilab.org
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Dan Thomas Major Sent: Saturday, January 26, 2002 11:40 AM To: modeller_usage@salilab.org 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
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Andrej Sali -
Dan Thomas Major