[phenixbb] bugs in dev 625

[Tom Terwilliger]

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 at 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:

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

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