[phenixbb] Can't autobuild after autosol?
Francis E Reyes
Francis.Reyes at Colorado.EDU
Mon May 19 17:00:09 PDT 2008
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
>>
>> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>>
>> 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
---------------------------------------------
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
More information about the phenixbb
mailing list