[phenixbb] phenix.mr_rosetta not running "prerefine"

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Oct 11 11:43:37 PDT 2011


Hi Laurie,

The problem is that mr_rosetta needed a pdb file name with more than 4
characters before the ".pdb" for this shortcut of generating pre-refined
models to work (the Rosetta routine requires a longer file name).  So if
you rename your PDB file this should run (it does on my machine.)  I will
fix mr_rosetta so that it can take your PDB file.

All the best,
Tom T


>> On Tue, Oct 11, 2011 at 12:33 PM, Thomas C. Terwilliger <
>> terwilliger at lanl.gov> wrote:
>>
>>> Hi Laurie,
>>>
>>> Yes, it is not doing anything.  There is something that didn't work in
>>> the
>>> inputs. Can you send me your fasta and PDB files and I'll just run it
>>> here
>>> to see what is wrong?
>>>
>>> Thanks!
>>> -Tom T
>>>
>>> >> OK - I am also sending:
>>> >>
>>> >>
>>> /netscr/bettsl/rosetta_test/MR_ROSETTA_2/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log
>>> >>
>>> >> On Tue, Oct 11, 2011 at 12:01 PM, Thomas C. Terwilliger <
>>> >> terwilliger at lanl.gov> wrote:
>>> >>
>>> >>> Hi Laurie,
>>> >>>
>>> >>> Yes, something didn't work it all right. Can you send me, off-list,
>>> this
>>> >>> log file:
>>> >>>
>>> >>>
>>> >>>
>>> /netscr/bettsl/rosetta_test/MR_ROSETTA_1/GROUP_OF_PLACE_MODEL_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log
>>> >>>
>>> >>> which I am guessing has some kind of error message in it.
>>> >>>
>>> >>> Thanks!
>>> >>> -Tom T
>>> >>>
>>> >>> >> Hi - I tried the little prerefine without any data script in your
>>> >>> >> documentation - I don't think it's working right.  I attach the
>>> >>> script
>>> >>> >> file
>>> >>> >> that I made (prerefine.dat) and the RUN_FILE_1.log.
>>> >>> >>
>>> >>> >> I can send more info offline if need be.
>>> >>> >>
>>> >>> >> Thanks
>>> >>> >>
>>> >>> >> LAurie Betts
>>> >>> >> _______________________________________________
>>> >>> >> phenixbb mailing list
>>> >>> >> phenixbb at phenix-online.org
>>> >>> >> http://phenix-online.org/mailman/listinfo/phenixbb
>>> >>> >>
>>> >>>
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>>>
>>>
>>



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