[phenixbb] Question about overall_best history

Tom Terwilliger terwilliger at lanl.gov
Thu Nov 20 07:12:59 PST 2008

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/ 
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:  
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/ 

Starting mtz file: /net/firebird/scratch1/terwill/run_111608a/MAD/ 
Sequence file: /net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/ 
File with locations where density is to be truncated: /net/firebird/ 

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  
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: 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: 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
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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