[phenixbb] composite omit map

[Tom Terwilliger]

Hi Jianghai,

If you use the AutoBuild wizard and specify Yes to Full_omit, then there 
will be a map produced in the subdirectory FULL_OMIIT called

resolve_composite_map.mtz

This will be coefficients for a composite omit map.  In this process you 
can specify whether to rebuild the model, how to do so, whether to refine 
etc. To just get an omit map you don't want to rebuild or refine.
-Tom T


09:09 AM 10/23/2006 -0700, you wrote:
>Content-Language: en
>Content-Type: multipart/alternative; boundary="--29c113a967c840d913a4"
>
> > 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>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
> > +++++++++++++++++++++++++++++++
> >
> >
> >
> >
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>phenixbb at phenix-online.org
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: 
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TB Structural Genomics Consortium web site: http://www.tbgenomics.org