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

Pavel Afonine pafonine at lbl.gov
Thu Mar 12 08:24:08 PDT 2015

Hi Phoebe,

I'm always interested to have a look at unusual cases... Often this 
builds knowledge and helps to improve methodology. Would you mind 
sending me files (data and model) so that I can investigate what's going on?


On 3/12/15 8:18 AM, Phoebe A. Rice wrote:
> I've been refining a 3.4A structure (now using dev-1951) and find that 
> anything besides TLS (with multiple groups at least) makes Rs go up. 
>  A lot.  And I am asking it to optimize weights.
> ++++++++++++++++++++++++++++++++++++++++++
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
> PRice at uchicago.edu <mailto:PRice at uchicago.edu>
> ------------------------------------------------------------------------
> *From:* phenixbb-bounces at phenix-online.org 
> [phenixbb-bounces at phenix-online.org] on behalf of Pavel Afonine 
> [pafonine at lbl.gov]
> *Sent:* Thursday, March 12, 2015 12:35 AM
> *To:* 李翔; PHENIX user mailing list
> *Subject:* Re: [phenixbb] Group B factor refinement not working for 
> low resolution data
> 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.
> Pavel
> 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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