<BODY contentEditable=true onload=parent.init()><P>> I have a few questions about phenix.refine and I couldn't find the <BR>> answer in the manual. </P>
<P>> 1) How to generate the ligand library in phenix.refine? </P>
<P>Try the wiki:</P>
<P><A href="http://www.phenix-online.org/phenix_wiki">http://www.phenix-online.org/phenix_wiki</A></P>
<P>Check under the heading 'refinement'</P>
<P><BR>> 2) Can phenix.refine calculate an OMIT COMPOSITE map? </P>
<P>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.</P>
<P><BR>> 3) When I used ML as the target, I couldn't find the output of LLG <BR>> or <BR>> similar number in the log file. How do I know the refinement is <BR>> converged? <BR><BR>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.</P>
<P>HTH</P>
<P>P</P>
<P><BR>> Thanks. <BR>> <BR>> Jianghai <BR>> <BR>> +++++++++++++++++++++++++++++++ <BR>> Jianghai Zhu, Ph.D <BR>> CBR Institute for Biomedical Research <BR>> Department of Pathology <BR>> Harvard Medical School <BR>> 200 Longwood Ave., Boston, MA 02115 <BR>> Ph: 617-278-3211 <BR>> Fx: 618-278-3232 <BR>> +++++++++++++++++++++++++++++++ <BR>> <BR>> <BR>> <BR>> </P></BODY>