Hi Tom I don't seem to have a exptl_fobs_phases_freeR_flags_1.mtz? Here's my output: chem171-152-dhcp:RBD_rebuild_xtalclear_SG96 francisreyes$ phenix.autosol show_summary PHENIX VERSION: 1.3b of 04-11-2007 PHENIX autosol Mon May 19 17:59:06 2008 The PHENIX developers include: P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo, J.C. Sacchettini, N.K. Sauter, L.C. Storoni, T.C. Terwilliger, P.H. Zwart If you use PHENIX please cite: Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.-W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K., Terwilliger, T.C. (2002). PHENIX: building new software for automated crystallographic structure determination. Acta Cryst. D58, 1948-1954. ------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol display_summary=True Carrying on with run 1 Going to instance.. 1 Restoring instance 1 PHENIX VERSION: 1.3b of 04-11-2007 --------------------------------------------------------------------------- AutoSol Run 1 Writing out files for solution # 1 -----------CURRENT SOLUTIONS FOR RUN 1 : ------------------- *** FILES ARE IN THE DIRECTORY: AutoSol_run_1_ **** Solution # 1 SCORE:68.3600668761 Dataset #1 FOM: 0.37 ---------------- Solution 1 using HYSS on AutoSol_run_1_/ ScalAveragedSG_92_PHX.sca_ano_1.sca. Dataset #1 Dataset number: 1 Dataset type: sad Datafiles used: ['AutoSol_run_1_/ScalAveragedSG_92_PHX.sca'] Sites: 2 (Already used for Phasing at resol of 3.4) Refined Sites: 4 NCS information in: AutoSol_1.ncs_spec Experimental phases in: phaser_1.mtz Density-modified phases in: resolve_1.mtz HA sites (PDB format) in: ha_1.pdb_formatted.pdb Sequence file in: seq_from_pdb.dat Scaling logfile in: dataset_1_scale.log HYSS logfile in: ScalAveragedSG_92_PHX.sca_ano_1.sca_hyss.log Phasing logfile in: phaser_1.log Density modification logfile in: resolve_1.log Score type: CC RFACTOR SKEW FOM NCS_OVERLAP Raw scores: 0.67 0.55 0.04 0.37 0.00 Z-scores: 42.52 15.50 2.96 7.38 0.00 Refined heavy atom sites (fractional): xyz 0.028 0.168 0.272 xyz 0.156 0.807 0.703 xyz 0.062 0.847 0.730 xyz 0.124 0.672 0.952 Solution # 2 SCORE:52.252588151 Dataset #1 FOM: 0.3 ---------------- NOTE: Output files for this solution not written out (in PDS only) Adjust 'number_of_solutions_to_display' (currently 1) to write them out. Solution 2 using HYSS on AutoSol_run_1_/ ScalAveragedSG_92_PHX.sca_ano_1.sca and taking inverse. Dataset #1 Dataset number: 1 Dataset type: sad Datafiles used: ['AutoSol_run_1_/ScalAveragedSG_92_PHX.sca'] Sites: 2 Refined Sites: 2 NCS information in: AutoSol_2.ncs_spec Experimental phases in: phaser_2.mtz HA sites (PDB format) in: ha_2.pdb_formatted.pdb Sequence file in: seq_from_pdb.dat Scaling logfile in: dataset_1_scale.log HYSS logfile in: ScalAveragedSG_92_PHX.sca_ano_1.sca_hyss.log Phasing logfile in: phaser_2.log Score type: CC RFACTOR SKEW FOM NCS_OVERLAP Raw scores: 0.65 0.61 -0.00 0.30 0.00 Z-scores: 40.76 5.45 -0.03 6.08 0.00 Refined heavy atom sites (fractional): xyz -0.031 -0.169 -0.271 xyz -0.155 -0.808 -0.706 --------------------------------------------------------------------------- On May 16, 2008, at 8:36 PM, Thomas C. Terwilliger wrote:

Hi Francis,

I'm sorry, it sure does look like your AutoSol run is done for run 3, and AutoBuild should indeed work in that case. I just made up a similar case on my computer and it worked as it was supposed to, so something has happened in your case that I don't understand.

To continue on as you wanted to, it would be best to just specify all the files for AutoBuild. They will all be in your AutoSol_run_3_/ directory. Something like

phenix.autobuild data=AutoSol_run_3_/phaser_1.mtz input_ha_file=AutoSol_run_3_/ha_1_formatted.pdb input_ncs_file=AutoSol_run_3_/AutoSol_1.ncs_spec input_map_file=AutoSol_run_3_/resolve_1.mtz input_refinement_file=AutoSol_run_3_/ exptl_fobs_phases_freeR_flags_1.mtz seq_file=seq.dat

should do it, where phaser_1, ha_1, AutoSol_1.ncs_spc, resolve_1 exptl...1.mtz all swap the 1 for whatever is the best solution (the first solution listed in AutoSol_summary.dat or with

phenix.autosol show_summary

If you are able to tar up the whole directory and let me have a look at it that would help me debug it so that this does not happen in the future.

All the best, Tom T ps. When we issue a new version of PHENIX (soon) be sure to upgrade as it has (mostly) fixed-up rebuild-in-place for nucleic acid model- building.

...

******************************************************************************** Failed to carry out AutoBuild_start:

Sorry, 'after_autosol' is set, but there were not any solutions from AutoSol found...please make sure that the highest-numbered AutoSol run is a completed run (you can use 'phenix.autosol show_runs' to see what runs are present and 'phenix.autosol delete_runs=xx' to remove any incomplete runs)

********************************************************************************

when issues with phenix.autobuild after_autosol

phenix.autosol show_runs gives..

------------------------------------------------------------ Starting AutoSol with the command:

phenix.autosol display_runs=True

---------------------------------------------------------------------------

List of runs for AutoSol

Run Title / Notes --------------------------------------------------------------------------- --------------------------------------------------------------------------- 3: Run 3 AutoSol Fri May 16 13:10:11 2008 STEP: finished Top solution: # 2 Dataset #1 Score: 27.84 FOM: 0.29 Built: 121 Side-chains: 0 Chains: 21 CC: 0.45 Sites: 4

Score type: CC RFACTOR SKEW FOM NCS_OVERLAP Raw scores: 0.61 0.59 0.03 0.30 0.00 Z-scores: 14.84 5.76 1.26 5.98 0.00

---------------------------------------------------------------------------

Does that mean an autosol run has completed?

Thanks

FR

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

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