[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
>>
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>>
>
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---------------------------------------------
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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