Now if I look at refine0.pdb generated from modeller, I have a problem.
As I mentioned before amino acids 25 and 50 are missing capping oxygens,
but modeller puts them on for me and refine0.pdb has two more atoms
than the initial
helices.ini.
***Here is the point, the added oxygen to amino acid 25 shifts the
labeling of all
of the atoms and their positions in the second alpha helix. ***
Look at and compare atoms 201 to 206 in the attached files to see
exactly what
I mean. Once you see, it will be clear that the optimization that
follows has a bit
of a tough time since all of the atoms in the second helix have shifted
positions.
Any hints about how to make this better?
Thanks,
Michael
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Michael Grabe, Ph.D.
Post-doctoral Fellow
Howard Hughes Medical Institute
University of California, San Francisco
533 Parnassus Ave.
San Francisco, CA 94143