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 +++++++++++++++++++++++++++++++