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.
Thank you _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb