Hi Katya, Yes, this is a bug, and it is fixed in our working version, but you don't have it yet. I'm sorry about that! The problem was basically that autobuild tries to cross the original model (with truncated side chains) with a rebuilt model, and it uses the whole-residue correlation coefficient to decide which is better. If one of the residues has no side chain (i.e., if you supplied a sequence file that is different than the starting model) the one with no side chain doesn't include the side-chain region in the correlation. Sometimes that gives a higher correlation and the one with the side chain never gets taken. It should instead use the correlation over the same region for the 2 models... All the best, -Tom T On Jan 21, 2009, at 2:43 PM, Katya Heldwein wrote:
Hi,
I ran phenix.autobuild with default setting (rebuild_in_place), and noticed that some side chains were gone in the resulting overall_best.pdb. That is, let's say, I started with Phe as residue 10. After rebuilding, the Phe10 is still called Phe in the output file, but the side chain atoms are gone, leaving residue 10 as Ala. This happened for several side chains, and I am at a loss for why this happened. Is this some kind of a bug?
Katya
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Ekaterina Heldwein, Ph.D.
Assistant Professor
Department of Molecular Biology and Microbiology
Tufts University School of Medicine
136 Harrison Ave
Boston, MA 02111
phone: 617-636-0858
fax: 617-636-0337
e-mail: [email protected]
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