VMD-L Mailing List
From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Fri Nov 19 2004 - 15:03:37 CST
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Hi Gavin,
after looking at your structures, I think that the problem arises
because the 3 monomers in the bad aligned "corners" are in different
order than in the other corners.
If I align your structures in reference to cnr1 using 'all' or 'resid
395 to 637' I get the same results as you, with cnr3, cnr5 and cnr7
misaligned. But using 'resid 395 to 637 and (chain G I)' only for
molecules cnr1 and cnr3 (to make it easier) aligns them perfectly. I
haven't try with the other two corners, but I guess is the same problem.
By the way I am not using the measure fit command, but the rmsdtt plugin
(the rmsd tool plugin should give the same results).
Hope this helps,
Luis
-- Luis Gracia, PhD Department of Physiology & Biophysics Weill Medical College of Cornell University 1300 York Avenue, Box 75 New York, NY 10021 Tel: (212) 746-6375 Fax: (212) 746-8690 lug2002_at_med.cornell.edu Gavin Murphy said the following on 11/18/04 23:37: > 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
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