Hi All, 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? 2) Can phenix.refine calculate an OMIT COMPOSITE map? 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? 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 +++++++++++++++++++++++++++++++
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 +++++++++++++++++++++++++++++++
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_wikihttp://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 +++++++++++++++++++++++++++++++
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] 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: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.tbgenomics.org
participants (3)
-
Jianghai Zhu -
Petrus H Zwart -
Tom Terwilliger