statistics output by phenix.refine
Hi, At the end of the log file output by phenix.refine, only R and Rfree are output. Is it possible to generate a statistical table which includes R, Rfree, FOM, LLG (total), LLG (free), rmsd (bond), rmsd (angle), ... for every refinement cycle? I want to monitor the progress of my refinement. 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, There are two comprehensive sections with statistics of all kinds (I think everything you're asking for): In the log file: ================= overall refinement statistics: step by step ================= And similar information in REMARK records in the output .pdb file: REMARK ****************** REFINEMENT STATISTICS STEP BY STEP ****************** Please let us know if you are interested in additional statistics. Ralf
Hi Ralf, Thanks for the answer. Apparently, I didn't read too carefully :) It has almost everything except LLG (total) and LLG (free). Is it possible to output those? 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 +++++++++++++++++++++++++++++++ On May 16, 2007, at 4:50 PM, Ralf W. Grosse-Kunstleve wrote:
Hi Jianghai,
There are two comprehensive sections with statistics of all kinds (I think everything you're asking for):
In the log file:
================= overall refinement statistics: step by step =================
And similar information in REMARK records in the output .pdb file:
REMARK ****************** REFINEMENT STATISTICS STEP BY STEP ******************
Please let us know if you are interested in additional statistics.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
LLG (total) and LLG (free)
If you refine with the "ml" or "mlhl" target, xray_target_w and xray_target_t are the values of the maximum likelihood targets. "w" is for work, "t" for test (i.e. free). We don't have the "total"; I have my doubts how meaningful the total would be. Ralf
participants (2)
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Jianghai Zhu -
Ralf W. Grosse-Kunstleve