> 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:

http://www.phenix-online.org/phenix_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.

HTH

P

> 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
> +++++++++++++++++++++++++++++++
>
>
>
>