[phenixbb] Autobuild Error

Tom Terwilliger terwilliger at lanl.gov
Wed Jun 1 07:44:03 PDT 2011


Dear Anand,

I'm sorry for the trouble!  This seems to be a failure in refinement during rebuilding.  It is possible that the error has been fixed since, so one solution is to download an even-more-recent version and try that.

Another possibility is to re-run the job with "debug=True" and then a more complete error message should be printed.

A third possibility is to send me (terwilliger at lanl.gov, off-list) all the files necessary to run the job and I will debug it here.

A fourth possibility is to look in the file

   /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/LAST.LOG

which may have some more clues.

All the best,
Tom T
  
On Jun 1, 2011, at 1:49 AM, B. Anand wrote:

> Dear All,
> 
>      I am using autobuild to rebuild the model after MR. However, it
> stops with the following error which am I not able to comprehend.
> Could you please shed some light on this error. Am using phenix
> version  1.7.1 (Release tag:743). Thanks.
> 
> With Best Regards,
> Anand
> 
> *************ERROR ENDING *******************
> 
> ********************************************************************************
> Failed to carry out AutoBuild_multiple_models:
> 
> 
> ********************************************************************************
> Sorry, a subprocess has failed...
> 
> END OF LOG FILE /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/RUN_FILE_1.log :
> 
> utoBuild  Run 1 Tue May 31 01:00:15 2011
> 
> Build cycle 1 of 16   method:rebuild
> Initial rebuild cycle: just combining previous models or copying
> over initial PDB file
> 
> Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1
> Refining model:  unrefined.pdb_1
> No refinement carried out (may need free R flags)
> Error message from phenix.refine:  'function' object has no attribute
> 'as_mtz_dataset'
> Refinement failed...
> *************ERROR ENDING *******************
> 
> ********************************************************************************
> Failed to carry out AutoBuild_build_cycle:
> 
> Initial phenix refinement of AutoBuild_run_1_/edited_pdb.pdb with
> exptl_fobs_phases_freeR_flags.mtz failed...quitting...
> /home/anand/Autobuild/5/AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/LAST.LOG
> may have additional information...
> 'function' object has no attribute 'as_mtz_dataset'
> ********************************************************************************
> 
> *************ERROR ENDING *******************
> 
> 
> 
> ********************************************************************************
> 
> *************ERROR ENDING *******************
> 
> 
> -- 
> B. Anand, Ph. D.
> Assistant Professor
> Department of Biotechnology
> Indian Institute of Technology Guwahati
> Guwahati 781039
> Assam, India
> Email: banand at iitg.ernet.in
>     anandbasub at gmail.com
> Phone: +91-361-258 2223
> Fax: +91-361-258 2249
> Web: http://www.iitg.ernet.in/banand/
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb


Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




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