<BODY contentEditable=true onload=parent.init()><P>Hi Jianghai,</P>
<P>thanks for your question !</P>
<P>> 1) How to generate the ligand library in phenix.refine? </P>
<P>I presume you mean topology and parameters file for a ligand in your model. Use eLBOW for this. For an example, check out the updated manual (click "Quick facts" link right next to phenix.refine documentation at <A href="http://www.phenix-online.org/download/cci_apps/">http://www.phenix-online.org/download/cci_apps/</A>).</P>
<P><BR>> 2) Can phenix.refine calculate an OMIT COMPOSITE map? </P>
<P>We do not calculate omit maps.</P>
<P>> 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 </P>
<P>The output PDB file with refined model contains more than enough information to be able to see if the refinement converged. For example, lloking for one below is enough:</P>
<P>1) Look for R/Rfree statistics from cycle to cycle;</P>
<P>2) Look for Targets (both xray and geometry) from cycle to cycle;</P>
<P>3) Look for deviations in ADP, coordinates</P>
<P>...</P>
<P><BR>Please don't hesitate to ask more questions if any!</P>
<P>Pavel.<BR></P></BODY>