[phenixbb] Question about overall_best history
Tom Terwilliger
terwilliger at lanl.gov
Thu Nov 20 08:03:08 PST 2008
Hi Mo,
Solve does have the option of using a cluster scattering factor
instead of the Ta by itself, but I haven't found it to be that useful
overall (you can't access this from within the autosol wizard but you
can with "phenix.solve", running it with a standard solve script).
Basically with the cluster compounds you have almost no phasing at a
certain resolution (about 4.5 A or so) no matter what you do. The
cluster scattering factor in principle accounts for this better than
just using a Ta. I think the reason the Ta occupancies and B factors
are still somewhat ok is that at lower resolutions a single-atom model
is not so far off, and you may not have full occupancy of the cluster
compound.
All the best,
Tom T
On Nov 20, 2008, at 8:31 AM, Mo Wong wrote:
> 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 <terwilliger at lanl.gov
> > wrote:
> 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: 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
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>
>
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