[phenixbb] Can't autobuild after autosol?

Thomas C. Terwilliger terwilliger at lanl.gov
Fri May 16 19:36:19 PDT 2008


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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>
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>
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