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
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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
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Does that mean an autosol run has completed?
Thanks
FR
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder
gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
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