[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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