[phenixbb] Disappearing density?

Kyle Dolan ktd at uchicago.edu
Mon Aug 9 14:08:57 PDT 2010

Hi all,

I attempted to improve the density around a helix and short linker region
using an average kick map but it didn't make things look much better. I then
tried creating a composite iterative-build omit map from phenix.autobuild,
but in this case the electron density around the helix/linker in question
largely disappeared! Is there another approach I can use that might improve
my maps, or should I start questioning my data? The dataset has >95%
completeness to 2.7 A so I am very curious as to why I am missing the
backbone now, where before I was only missing the side chain densities. One
thing I am wondering is if the problem could have something to do with
symmetry; the part of the map I am looking at may be close to a two-fold
crystallographic symmetry axis and I have been told that these regions tend
to be very noisy and hard to model--comments?


Kyle T. Dolan
Department of Biochemistry and Molecular Biology
The University of Chicago
ktd at uchicago.edu
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