[phenixbb] bad geometry problem

Pavel Afonine pafonine at lbl.gov
Tue Jun 19 21:10:53 PDT 2012

Hi Sarah,

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(bonds):0.02
>    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!
> best,
> Sarah

More information about the phenixbb mailing list