VMD-L Mailing List

From: Gavin Murphy (gavinm_at_caltech.edu)
Date: Thu Nov 18 2004 - 22:37:35 CST

Hello,
   I am working on the cubic core of pyruvate dehydrogenase. It has 8
corners, each made of 3 monomers. I am trying to align 7 of the 8
corners to one particular corner. I get bad alignments with three of
the corners, and I believe that it has to do with symmetry. They are
the corners that are diagnolly opposite one another on any given face.
All the other corners align well. I am using the
measure fit command. Is there a bug in the software, or am I missing
something? I could give out the pdb files to anyone who wants to
reproduce it.

Thank you,
Gavin Murphy