Hi,
Thank you for the e-mail.
It makes sense; I was thrown off by the fact that my MAP CCs for all
solutions are all so close but the FOM for the top scoring solution is much
lower (by about 0.1 overall, and by ~0.25 in the highest resol. shell) when
compared to the second top scoring solution. This probably relates to the
fact the the anomalous signal isn't too great beyond 4.5 while I'm trying to
phase beyond that, and that I'm using Ta for a TaBr cluster.
Which reminds me, how come when I phase using Ta instead of a TaBr cluster
the occupanies and B-factors don't blow up in SOLVE?
Thanks again!
On Thu, Nov 20, 2008 at 10:12 AM, Tom Terwilliger
Hi Mo, When you run AutoSol, the summary will tell you which is the best overall solution: see near the end of the AutoSol_run_1_/AutoSol_run_1_1.log file or the AutoSol_run_1_/AutoSol_summary.dat file which will look like:
-----------CURRENT SOLUTIONS FOR RUN 1 : -------------------
*** FILES ARE IN THE DIRECTORY: AutoSol_run_1_ ****
Solution # 28 BAYES-CC: 57.4 +/- 14.2 Dataset #1 SG: "C 1 2 1" FOM: 0.49
Solution 28 based on diff Fourier using denmod solution 7. Dataset #1 SG="C 1 2 1" Dataset number: 1 Dataset type: mad Datafiles used: ['/net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/high.sca', '/net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/infl.sca', '/net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/peak.sca'] Sites: 2 (Already used for Phasing at resol of 2.6) Refined Sites: 2 NCS information in: AutoSol_28.ncs_spec Experimental phases in: solve_28.mtz Experimental phases plus FreeR_flags for refinement in: exptl_fobs_phases_freeR_flags_28.mtz Density-modified phases in: resolve_28.mtz HA sites (PDB format) in: ha_28.pdb_formatted.pdb Sequence file in: sequence.dat Model in: refine_23.pdb
The best solution is listed first. So this is the one you want. In this example your "solve" file is solve_28.mtz. If you are running SAD phasing, then this will instead be a "phaser" file. Your "resolve" file is resolve_28.mtz.
In AutoBuild, there is no "solve_..".mtz, as experimental phases are fixed in those runs. The solve....mtz experimental phases from AutoSol are copied to a file like "exptl_fobs_phases_freeR_flags.mtz" and are used in density modification and refinement. The best density-modified phases are in the overall_best_denmod_map_coeffs.mtz, and the AutoBuild_run_1_/AutoBuild_summary.dat file will tell you which cycle they came from:
Summary of model-building for run 1 Sun Nov 16 21:33:01 2008 Files are in the directory: /net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/AutoBuild_run_1_/
Starting mtz file: /net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/AutoSol_run_1_/solve_28.mtz Sequence file: /net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/AutoSol_run_1_/sequence.dat File with locations where density is to be truncated: /net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/AutoSol_run_1_/ha_28.pdb_formatted.pdb
Best solution on cycle: 5 R/Rfree=0.22/0.31
Summary of output files for Solution 5 from build cycle 5
--- Model (PDB file) --- pdb_file: AutoBuild_run_1_/cycle_best_5.pdb
--- Refinement log file --- log_refine: AutoBuild_run_1_/cycle_best_5.log_refine
--- Model-building log file --- log: AutoBuild_run_1_/cycle_best_5.log
--- Model-map correlation log file --- log_eval: AutoBuild_run_1_/cycle_best_5.log_eval
--- 2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT --- refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_5.mtz
--- Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag --- hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz
--- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_1_/cycle_best_5.mtz
I hope that helps! -Tom T
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.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
On Nov 20, 2008, at 8:01 AM, Mo Wong wrote:
Hi all,
I'm sure this is in one of the log files (and written somewhere in the documentation), but I can't find which solve_*.mtz and which subsequent resolve_*.mtz were used to make overall_best_denmod_map_coeffs.mtz.
Could someone please tell me where I may find it.
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