[phenixbb] Group B factor refinement not working for low resolution data

Pavel Afonine pafonine at lbl.gov
Wed Mar 11 22:35:38 PDT 2015

Hello Xiang,

short answer: try refining with all defaults plus weight optimization. 
If that does not go well please send me data and model files and I will 
do my best to make it work.

Longer answer: the way B-factor restraints are implemented in 
phenix.refine (that you can learn about in corresponding paper) allows 
refining individual Bs at any resolution. So this is why this is the 
first choice to try. If that does not work it's best to a) let us know 
and b) try group B refinement.


On 3/11/15 7:30 PM, 李翔 wrote:
> Hi,
> I am working on my ~6A data with molecular replacement method. The MR 
> works out and after rigid body and xyz refinement the result is OK. 
> However, when I tried the ADP refinement with Group B factor option in 
> PHENIX GUI, the R factor significantly increased as well as the 
> B-factor. Any expert can help me to take a look and give some 
> suggestions please?
> Thank you very much for your help!
> Sincerely,
> Xiang
> -- 
> Li Xiang
> Department of chemistry,
> University of Michigan
> Email:lixiang1642 at gmail.com <mailto:lixiang1642 at gmail.com>
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