[phenixbb] Fix rotamers

Jeff Headd jjheadd at lbl.gov
Fri Apr 16 13:16:08 PDT 2010

Hi Jason,

Yes, you are on the right track.  For each sidechain that is
corrected, the method rotates each torsion angle moving out from the
backbone looking for the best real-space fit to the density.  Once the
sidechain has been fit, there is real-space refinement.  The maps are
updated throughout to allow for the best possible map for each

Perhaps Pavel will chime in with any other details that I'm forgetting.


On Fri, Apr 16, 2010 at 12:52 PM, Jason C Porta <jporta at unmc.edu> wrote:
> Hi everyone,
> I'm currently looking for some info on the "fix rotamer" option in
> phenix.refine. I searched the online docs and board archives, but came up
> empty.
> Could someone please explain to me how the software carries out the rotamer
> refinement? From the log file it looks like a map is calculated for each
> rotamer followed by a real-space refinement? Am I thinking on the right
> track?
> Thanks in advance!
> Jason
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