<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:Courier New,courier,monaco,monospace,sans-serif;font-size:10pt"><div>Hi Oliver,<br>This bug is now fixed. The fix will appear in build 630<br>tonight.<br>If you want to patch your current installation, edit the<br>file $PHENIX/cctbx_project/mmtbx/twinning/twin_f_model.py<br>and insert the line<br><br>import libtbx.path<br><br>at the top.<br><br>Ralf<br></div><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><div style="font-family: Courier New,courier,monaco,monospace,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><b><span style="font-weight: bold;">From:</span></b> Tom Terwilliger <terwilliger@lanl.gov><br><b><span style="font-weight: bold;">To:</span></b> PHENIX user mailing list
<phenixbb@phenix-online.org><br><b><span style="font-weight: bold;">Sent:</span></b> Tue, January 4, 2011 10:46:13 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [phenixbb] bugs in dev 625<br></font><br>
Dear Oliver,<div><br></div><div>Thank you for the bug report, and I'm sorry for the problem!</div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Might it be possible to send me the inputs that you used and the exact command you ran phenix.autobuild with (directly at <a rel="nofollow" ymailto="mailto:terwilliger@lanl.gov" target="_blank" href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>, not to the list)? If so, I can run it and figure out what is going
wrong, and hopefully fix it right away.</div><div><br></div><div>Thanks very much!</div><div>-Tom T</div><div><br><div><div>On Jan 4, 2011, at 6:08 AM, Weiergr�ber, Oliver H. wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hello,<br><br>trying to use phenix.autobuild (command line version, didn't try the gui) in dev 625, I encountered the following error:<br><br>############################################<br>Build cycle 1 of 6 method:rebuild<br>Initial rebuild cycle: just combining previous models or copying<br>over initial PDB file<br><br>Using edited_pdb.pdb for rebuild, copied to unrefined.pdb_1<br>Refining model: unrefined.pdb_1<br>No refinement carried out (may need free R flags)<br>Error message from phenix.refine: global name 'libtbx' is not defined<br>Refinement failed...<br>############################################<br><br>If invoked directly, phenix.refine seems to run fine, so there
may be a problem with scripting in the autobuild wizard.<br><br>Regards,<br>Oliver<br><br><br>================================================<br> PD Dr. Oliver H. Weiergr�ber<br> Institut f�r Strukturbiologie und Biophysik<br> ISB-3: Strukturbiochemie<br> Tel.: +49 2461 61-2028<br> Fax: +49 2461 61-1448<br>================================================<br><br>------------------------------------------------------------------------------------------------<br>------------------------------------------------------------------------------------------------<br>Forschungszentrum Juelich GmbH<br>52425 Juelich<br>Sitz der Gesellschaft: Juelich<br>Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498<br>Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher<br>Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),<br>Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,<br>Prof. Dr. Sebastian M.
Schmidt<br>------------------------------------------------------------------------------------------------<br>------------------------------------------------------------------------------------------------<br>_______________________________________________<br>phenixbb mailing list<br><a rel="nofollow" ymailto="mailto:phenixbb@phenix-online.org" target="_blank" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><span><a target="_blank" href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a></span><br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px;"><div><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a rel="nofollow" ymailto="mailto:terwilliger@LANL.gov" target="_blank" href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br><span>Fax: 505-665-3024 SOLVE web site: <a target="_blank" href="http://solve.lanl.gov">http://solve.lanl.gov</a></span><br>PHENIX
web site: http:<a target="_blank" href="http://www.phenix-online.org">www.phenix-online.org</a><br><span>ISFI Integrated Center for Structure and Function Innovation web site: <a target="_blank" href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a></span><br><span>TB Structural Genomics Consortium web site: <a target="_blank" href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></span></div><div><span>CBSS Center for Bio-Security Science web site: <a target="_blank" href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a></span><br><br></div></div></div></div><br></div></span><br class="Apple-interchange-newline">
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