Hi,<br><br>Thank you for the e-mail.<br><br>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&#39;t too great beyond 4.5 while I&#39;m trying to phase beyond that, and that I&#39;m using Ta for a TaBr cluster.<br>
<br>Which reminds me, how come when I phase using Ta instead of a TaBr cluster the occupanies and B-factors don&#39;t blow up in SOLVE?<br><br>Thanks again!<br><br><div class="gmail_quote">On Thu, Nov 20, 2008 at 10:12 AM, Tom Terwilliger <span dir="ltr">&lt;<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div style="">Hi Mo,<div><br></div><div>When you run AutoSol, the summary will tell you which is the best overall solution: &nbsp;see near the end of the AutoSol_run_1_/AutoSol_run_1_1.log file or the</div>
<div>AutoSol_run_1_/AutoSol_summary.dat file which will look like:</div><div><br></div><div><div>-----------CURRENT SOLUTIONS FOR RUN 1 : -------------------</div><div><br></div><div>&nbsp;*** FILES ARE IN THE DIRECTORY: AutoSol_run_1_ ****</div>
<div><br></div><div><br></div><div><br></div><div>Solution # 28 &nbsp;BAYES-CC: 57.4 +/- 14.2 Dataset #1 &nbsp; SG: &quot;C 1 2 1&quot; &nbsp; FOM: 0.49</div><div><br></div><div>Solution 28 based on diff Fourier using denmod solution 7. Dataset #1 SG=&quot;C 1 2 1&quot;</div>
<div>Dataset number: 1</div><div>Dataset type: mad</div><div>Datafiles used: [&#39;/net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/high.sca&#39;, &#39;/net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/infl.sca&#39;, &#39;/net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/peak.sca&#39;]</div>
<div>Sites: 2 (Already used for Phasing at resol of 2.6) &nbsp; &nbsp; &nbsp;Refined Sites: 2</div><div>NCS information &nbsp;in: AutoSol_28.ncs_spec</div><div>Experimental phases in: solve_28.mtz</div><div>Experimental phases plus FreeR_flags for refinement in: exptl_fobs_phases_freeR_flags_28.mtz</div>
<div>Density-modified phases in: resolve_28.mtz</div><div>HA sites (PDB format) in: ha_28.pdb_formatted.pdb</div><div>Sequence file in: sequence.dat</div><div>Model in: refine_23.pdb</div><div><br></div><div><br></div><div>
The best solution is listed first. So this is the one you want. In this example your &quot;solve&quot; file is solve_28.mtz. &nbsp;If you are running SAD phasing, then this will instead be a &quot;phaser&quot; file. &nbsp;Your &quot;resolve&quot; file is resolve_28.mtz.</div>
<div><br></div><div><br></div><div>In AutoBuild, there is no &quot;solve_..&quot;.mtz, as experimental phases are fixed in those runs. &nbsp;The solve....mtz experimental phases from AutoSol are copied to a file like &quot;exptl_fobs_phases_freeR_flags.mtz&quot; and are used in density modification and refinement. &nbsp;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:</div>
<div><br></div><div><div>Summary of model-building for run 1 &nbsp;Sun Nov 16 21:33:01 2008</div><div>Files are in the directory: &nbsp;/net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/AutoBuild_run_1_/</div><div><br></div><div>
<br></div><div>Starting mtz file: /net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/AutoSol_run_1_/solve_28.mtz</div><div>Sequence file: /net/firebird/scratch1/terwill/run_111608a/MAD/gene-5/AutoSol_run_1_/sequence.dat</div>
<div>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</div><div><br></div><div>Best solution on cycle: 5 &nbsp; &nbsp;R/Rfree=0.22/0.31</div>
<div><br></div><div>Summary of output files for Solution 5 from build cycle 5</div><div><br></div><div>--- &nbsp;Model (PDB file) &nbsp;---</div><div>pdb_file: AutoBuild_run_1_/cycle_best_5.pdb</div><div><br></div><div>--- &nbsp;Refinement log file ---</div>
<div>log_refine: AutoBuild_run_1_/cycle_best_5.log_refine</div><div><br></div><div>--- &nbsp;Model-building log file ---</div><div>log: AutoBuild_run_1_/cycle_best_5.log</div><div><br></div><div>--- &nbsp;Model-map correlation log file ---</div>
<div>log_eval: AutoBuild_run_1_/cycle_best_5.log_eval</div><div><br></div><div>--- &nbsp;2FoFc and FoFc map coefficients from refinement 2FOFCWT PH2FOFCWT FOFCWT PHFOFCWT ---</div><div>refine_map_coeffs: AutoBuild_run_1_/cycle_best_refine_map_coeffs_5.mtz</div>
<div><br></div><div>--- &nbsp;Data for refinement FP SIGFP PHIM FOMM HLAM HLBM HLCM HLDM FreeR_flag ---</div><div>hklout_ref: AutoBuild_run_1_/exptl_fobs_phases_freeR_flags.mtz</div><div><br></div><div>--- &nbsp;Density-modified map coefficients FP PHIM FOM ---</div>
<div>hklout_denmod: AutoBuild_run_1_/cycle_best_5.mtz</div><div><br></div><div><br></div><div>I hope that helps!</div><div>-Tom T</div><div><br></div></div><div> <span style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div style="">
<div><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel:&nbsp; 505-667-0072&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; email: <a href="mailto:terwilliger@LANL.gov" target="_blank">terwilliger@LANL.gov</a><br>
Fax: 505-665-3024&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; SOLVE web site:&nbsp;<a href="http://solve.lanl.gov" target="_blank">http://solve.lanl.gov</a><br>PHENIX web site: http:<a href="http://www.phenix-online.org" target="_blank">www.phenix-online.org</a><br>
ISFI Integrated Center for Structure and Function Innovation web&nbsp;site:&nbsp;<a href="http://techcenter.mbi.ucla.edu" target="_blank">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site:&nbsp;<a href="http://www.doe-mbi.ucla.edu/TB" target="_blank">http://www.doe-mbi.ucla.edu/TB</a></div>
<div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss" target="_blank">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></div></span><br> </div><br><div><div><div></div>
<div class="Wj3C7c"><div>On Nov 20, 2008, at 8:01 AM, Mo Wong wrote:</div><br></div></div><blockquote type="cite"><div><div></div><div class="Wj3C7c">Hi all,<br><br>I&#39;m sure this is in one of the log files (and written somewhere in the documentation), but I can&#39;t find which solve_*.mtz and which subsequent resolve_*.mtz were used to make overall_best_denmod_map_coeffs.mtz.<br>
 <br>Could someone please tell me where I may find it.<br><br>Thank you<br></div></div> _______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote></div><br></div></div><br>_______________________________________________<br>

phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<a href="http://www.phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br>
<br></blockquote></div><br>