[phenixbb] Disappearing side chains after autobuilding

Katya Heldwein katya.heldwein at tufts.edu
Wed Jan 21 13:43:15 PST 2009


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?



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: katya.heldwein at tufts.edu

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