[phenixbb] a few questions

Petrus H Zwart PHZwart at lbl.gov
Mon Oct 23 09:09:38 PDT 2006

> I have a few questions about phenix.refine and I couldn't find the 
> answer in the manual. 
> 1)  How to generate the ligand library in phenix.refine? 
Try the wiki:
Check under the heading 'refinement'

> 2) Can phenix.refine calculate an OMIT COMPOSITE map? 
No. There is something that is called a full omit map, which is something close to a composite omit map. I am not sure how to produce this, maybe Tom Terwilliger can be of assistence there.

> 3) When I used ML as the target, I couldn't find the output of LLG 
> or  
> similar number in the log file.  How do I know the refinement is  
> converged? 

Convergence typically depends on the criteria set. In macro molceular refinement, this criteria is usually defined by the number of cycles. In any case, stagnation of R-free and a statisfactory validation of the model is usually a good indication that the end is near.

> Thanks. 
> Jianghai 
> +++++++++++++++++++++++++++++++ 
> Jianghai Zhu, Ph.D 
> CBR Institute for Biomedical Research 
> Department of Pathology 
> Harvard Medical School 
> 200 Longwood Ave., Boston, MA 02115 
> Ph: 617-278-3211 
> Fx: 618-278-3232 
> +++++++++++++++++++++++++++++++ 
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