[phenixbb] bad geometry problem
pafonine at lbl.gov
Tue Jun 19 21:10:53 PDT 2012
if you send me the model and data files (off-list) I will be happy to
have a look and may be I come up with an idea of how to improve things.
I've seen quite a few cases that fit your description and in most of
them there was a clear reason for geometry being poor. Knowing it is a
key. So hopefully your case is not an exception.
On 6/19/12 1:17 AM, Qian Sarah wrote:
> Hi, this may not be a new problem, but I tried every stretagy that I
> know from bb, but the geometry is still very bad. So I wish I can get
> some help from here.
> Crystal information:
> SAD data. Resolution 3.0. There is no anisotropy in the data.
> R/Rfree : 22.7/26.8 (Rfree-flag is always from the Refine_data.mtz
> file generated after the first refinement.)
> RMS(angles): 1.453
> Ramachandran outliers: 3.0%
> Ramachandran favored: 91.2%
> Rotamer outliers: 18.7% !!
> Clashscore: 31.84
> overall score: 3.47
> I tried different strategies, like autobuild and then refine; set
> wxu/wxc=0.3/0.3; turn on "Ramachandran restrains", "fix bad sidechain
> romaters"etc, however the paramters are still very bad, especially the
> rotamer outliers. Then I rebuild them manually in coot,after
> refinement the parameters are even worse.
> p.s. phenix version: phenix-1.7.3-dev-1046.
> Thank you very much!
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