[phenixbb] mr_rosetta problems

[Andreas Förster]

Hi Ian,

I had a similar issue once.  Check that your fragment files start with a 
line reading

  position:            1 neighbors:          200

or something like this.  If there's html code (download artifact), 
remove it.  Same at the end of the files.  Last line should be blank and 
before that, only fragments.



Andreas



On 07/08/2012 5:52, Terwilliger, Thomas C wrote:
> Hi Ian,
>
> I think this part of the error message is the best hint:
>
> finished reading top 0 0mer fragments from
> file/dataFiles/aat000_03_05.200_v1_3
>
> I am guessing there is something odd about the fragment file all right.
> You could try supplying this file in one of the tests and see if it
> causes the test to fail:
>
> phenix_regression.wizards.test_command_line_rosetta_quick test_prerefine
>
> then:...
>
> cd test_prerefine
> phenix.mr_rosetta seq_file=seq.dat search_models=coords1.pdb
> start=place_model stop=place_model data=fobs.mtz is_sub_process=True
> already_placed=true refine_after_mr=False run_prerefine=True
> number_of_prerefine_models=1 rosetta_fixed_seed=1571
> fragment_files=/Users/terwill/unix/PHENIX/phenix-dev-894/phenix/phenix/rosetta/dummy_fragments_file_3.gz
> fragment_files=/Users/terwill/unix/PHENIX/phenix-dev-894/phenix/phenix/rosetta/dummy_fragments_file_9.gz
>
> Then, try above with your fragment files...
>
> That might point out the problem!
> All the best,
> Tom T
>
>
>
>
>
>
> *From:* phenixbb-bounces at phenix-online.org
> [phenixbb-bounces at phenix-online.org] on behalf of Ian Slaymaker
> [slaymake at usc.edu]
> *Sent:* Tuesday, August 07, 2012 10:21 AM
> *To:* phenixbb at phenix-online.org
> *Subject:* [phenixbb] mr_rosetta problems
>
> I am trying to get mr_rosetta working on our cluster and am running into
> some problems I am not sure how to solve. The
> phenix_regression.wizards.test_command_line_rosetta_quick_tests tests
> went smoothly were completed.
>
> However, my first test run with all the defaults (not submitted to
> multiple processors) using my reflection file, HHR analysis file,
> sequence file, and the 2 fragment files failed with the below errors. I
> checked all the files, and it seems this is a problem with the fragment
> files but I am not sure exactly what they are supposed to look like.
>
> I thought it could be because our cluster doesnt have access to any
> outside networks...is this a problem with rosetta not being able to
> download pdb files? if so, is there a way to supply them internally?
> The aligned model looks somewhat what I expected it to (same beta sheet
> arrangement) but it seems to be incomplete.
> Any help would be very much appreciated!
>
>
>
> Splitting work into 100 jobs and running with 1 processors using sh
> background=None in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1
>
> Starting job 1...Log will be: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log
>
> ******************* ERROR ENDING ***************
> mr_rosetta failed...
>
> ********************************************************************************
> Sorry, a subprocess has failed...
>
> END OF LOG FILE /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_FILE_1.log :
>
> to match the actual PDB sequence:
> (protein sequence)
> New alignment line 4 for PDB:
> (protein sequence)
>
>
> Start position of target sequence in sequence file:  0
>
> Aligned model for comparison: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/aligned_model.pdb
> Log for rebuilding: /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log
>
> **************ERROR ENDING**********************
> Failed to run REBUILD...see log file in /MR_ROSETTA_1/GROUP_OF_ROSETTA_REBUILD_1/RUN_1/REBUILD_IN_SETS_1/RUN_1/WORK_1/rebuild.log
>
>
> The rebuild log had repeats of several errors that I am not sure how to address:
>
> core.conformation.Conformation: [ WARNING ] missing heavyatom:  CD2 on residue PHE 3 (repeated several times)
>
> core.fragments.ConstantLengthFragSet: line too short: Skipping line ' (repeated several times)
>
>
> core.fragments.ConstantLengthFragSet: finished reading top 0 0mer
> fragments from file/dataFiles/aat000_03_05.200_v1_3
> protocols.loops.loops_main: Frag libraries debug none 1
>
>
>
>
>
>
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-- 
         Andreas Förster, Research Associate
         Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
             http://www.msf.bio.ic.ac.uk