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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;"><span class="Apple-style-span" style="font-family: tahoma, sans-serif; font-size: medium; ">Hi Ian,</span>
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<div><span class="Apple-style-span" style="font-family: tahoma, sans-serif; font-size: medium; ">I think this part of the error message is the best hint:</span></div>
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<div><span class="Apple-style-span" style="font-family: tahoma, sans-serif; font-size: medium; ">finished reading top 0 0mer fragments from file/dataFiles/aat000_03_05.200_v1_3</span></div>
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<div><font class="Apple-style-span" face="tahoma, sans-serif" size="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:</font></div>
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<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">phenix_regression.wizards.test_command_line_rosetta_quick test_prerefine</span></font></div>
<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; "><br>
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<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">then:...</span></font></div>
<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; "><br>
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<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">cd test_prerefine</span></font></div>
<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">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</span></font></div>
<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; "><br>
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<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">Then, try above with your fragment files...</span></font></div>
<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; "><br>
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<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">That might point out the problem!</span></font></div>
<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">All the best,</span></font></div>
<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">Tom T</span></font></div>
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<div id="divRpF366199" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Ian Slaymaker [slaymake@usc.edu]<br>
<b>Sent:</b> Tuesday, August 07, 2012 10:21 AM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] mr_rosetta problems<br>
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<div><span style="font-family:arial,helvetica,sans-serif">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 </span><span style="font-family:arial,helvetica,sans-serif">phenix_regression.wizards.test_command_line_rosetta_quick_tests
tests went smoothly were completed. </span></div>
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<div><span style="font-family:arial,helvetica,sans-serif">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 </span><span style="font-family:arial,helvetica,sans-serif">but I am not sure exactly what they are supposed to look like</span><span style="font-family:arial,helvetica,sans-serif">.</span></div>
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<div>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? </div>
<div>The aligned model looks somewhat what I expected it to (same beta sheet arrangement) but it seems to be incomplete.</div>
<div>Any help would be very much appreciated!</div>
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<pre><font face="arial, helvetica, sans-serif">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
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<pre><font face="arial, helvetica, sans-serif"><br></font></pre>
<pre><font face="arial, helvetica, sans-serif">The rebuild log had repeats of several errors that I am not sure how to address:</font></pre>
<pre><font face="tahoma, sans-serif">core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 3 (repeated several times)</font></pre>
<pre><font face="tahoma, sans-serif">core.fragments.ConstantLengthFragSet: line too short: Skipping line ' (repeated several times)</font></pre>
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<div><font face="tahoma, sans-serif">core.fragments.ConstantLengthFragSet: finished reading top 0 0mer fragments from file/dataFiles/aat000_03_05.200_v1_3</font></div>
<div><font face="tahoma, sans-serif">protocols.loops.loops_main: Frag libraries debug none 1</font></div>
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