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 <[email protected]> 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: [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
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