cis proline

Xin Jia xjia at LJCRF.EDU
Wed Nov 20 18:51:40 EST 1996

Dear xplor users:

I have a question about cis- proline conformation in the structure
calculations.  I found if a proline residue is a trans- conformation, 
the calculation is fine. But if it is the cis-, after refinement, 
it turn to be a distorted trans- with some typical distance violations.
The topology files I have used were either from the
standard xplor library or the one modified by Dr. Michael Nilges
for improving prolines. These files include patches
which allow the convertion from trans- to cis- peptide bond.
As a control, I have also used the program "Discover" (Biosym) to
refine the structure. I got almost perfect cis- conformation from
the same starting structure and experimental constraints.
I wonder why? Any comment and suggestion will be very helpful.
Thanks in advance.

Xin Jia
La Jolla Cancer Research Center
The Burhman Institute

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