Hello, trying to use phenix.autobuild (command line version, didn't try the gui) in dev 625, I encountered the following error: ############################################ Build cycle 1 of 6 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: global name 'libtbx' is not defined Refinement failed... ############################################ If invoked directly, phenix.refine seems to run fine, so there may be a problem with scripting in the autobuild wizard. Regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institut für Strukturbiologie und Biophysik ISB-3: Strukturbiochemie Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
Dear Oliver, Thank you for the bug report, and I'm sorry for the problem! I'm not quite sure what occurred here. Our automatic tests for dev 625 all passed fine (except some minor printout changes in phenix.mr_rosetta) and these include a full set of tests on phenix.autobuild. I am guessing that perhaps: (1) there was something unusual in this run, maybe something in your pdb file, (2) this triggered an unusual path in phenix.autobuild, and (3) in this unusual path there is an error where libtbx is not defined, leading to your output. Might it be possible to send me the inputs that you used and the exact command you ran phenix.autobuild with (directly at terwilliger@lanl.gov, not to the list)? If so, I can run it and figure out what is going wrong, and hopefully fix it right away. Thanks very much! -Tom T On Jan 4, 2011, at 6:08 AM, Weiergräber, Oliver H. wrote:
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger@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
participants (3)
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Ralf W. Grosse-Kunstleve -
Tom Terwilliger -
Weiergräber, Oliver H.