[phenixbb] real space refinement or fix rotamers

Jeff Headd jjheadd at lbl.gov
Thu Oct 14 01:06:27 PDT 2010

Hi Helene,

For fixing bad rotamers it is best to first try the "fix bad sidechain
rotamers" option first.  Often these residues are systematically
misfit nearly flipped 180 degrees and regular refinement or real space
refinement are not powerful enough to escape the false minima.  If any
bad rotamers remain after automatic correction it is best to try and
fix them by hand in a graphical program such as Coot.


On Thu, Oct 14, 2010 at 8:34 AM,  <helene.krueger at staff.uni-marburg.de> wrote:
> Hi,
> I want to fit bad fitting residues into electron density of my 2.0 A
> dataset. To do so should I use the "real space" option or the "fix bad
> sidechain rotamers" option? or both?
> Thanks
> Helene
> --
> Helene Köster
> Philipps-Universität Marburg
> Institute of Pharmaceutical Chemistry
> AG Klebe
> Marbacher Weg 6
> 35032 Marburg, Germany
> Phone: +49-6421-28-25908
> Mail: helene.krueger at staff.uni-marburg.de
> www.agklebe.de
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