<div>I ran the suggested test, and checked my fragment files. The fragment files seem to be spic and span, but the test still errored out with this and the rebuild.log file looked the same. </div><div>My fragment files look like this :</div>
<div><div> </div><div>position: 1 neighbors: 200</div><div><br></div><div> 1je5 A 137 M L -94.840 117.510 -178.319 2.237 10.852 31.857 3 0.000 P 1 F 1</div><div> 1je5 A 138 E L -71.213 -39.327 177.116 2.237 10.852 31.857 3 0.000 P 1 F 1</div>
<div> 1je5 A 139 D L -112.228 93.181 -175.069 2.237 10.852 31.857 3 0.000 P 1 F 1</div><div> 1je5 A 140 V L -70.333 120.424 178.205 2.237 10.852 31.857 3 0.000 P 1 F 1</div></div><div>
<br></div><div>Starting mr_rosetta_rebuild</div><div>Date: Tue Aug 7 10:15:26 2012</div><div>Directory: /test_prerefine</div><div><br></div><div>HOST = hpc-cmb</div><div>HOSTTYPE = x86_64-linux</div><div>USER = slaymake</div>
<div>PID = 30481</div><div>Checking rosetta paths:</div><div> rosetta binary: /home/cmb-04/rr/slaymake/rosetta/rosetta3.4/rosetta_source/bin/mr_protocols.default. linuxgccrelease</div>
<div> database_dir: /home/cmb-04/rr/slaymake/rosetta/rosetta3.4/rosetta_database</div><div> script_dir: /home/cmb-04/rr/slaymake/rosetta/rosetta3.4/rosetta_source/src/apps/public/electron_dens ity</div>
<div>pilot_script_dir: /home/cmb-04/rr/slaymake/rosetta/rosetta3.4/rosetta_source/src/apps/pilot/frank/</div><div><br></div><div>Sequence rewritten to /test_prerefine/WORK_2/EDITED_seq.dat :</div>
<div> > sequence information</div><div>AQLMDMRD</div><div><br></div><div>Changing to work directory: /test_prerefine/WORK_2</div><div><br></div><div><br></div><div>Rebuilding the model/test_prerefine/coords1.pdb</div>
<div>
with rosetta</div><div>Running mr_rosetta_rebuild without map information</div><div><br></div><div>Generating 1 rebuilt models</div><div>================================================================================</div>
<div>Reading model from/test_prerefine/coords1.pdb</div><div>================================================================================</div><div>ALIGNMENT LINES:</div><div>## TARGET coord</div><div># hhsearch</div>
<div>scores_from_program: 0 1.00</div><div>0 AQLMDMRD</div><div>0 -QLMDMRD</div><div>--</div><div><br></div><div>Alignment file matches PDB file</div><div>Start position of target sequence in sequence file: 0</div><div>
<br>
</div><div>Aligned model for comparison: /test_prerefine/WORK_2/WORK_1/aligned_model.pdb</div><div>Log for rebuilding: /test_prerefine/WORK_2/WORK_1/rebuild.log</div><div><br></div><div>******************* ERROR ENDING ***************</div>
<div>Failed to run REBUILD...see log file in /test_prerefine/WORK_2/WORK_1/rebuild.log</div><div><br></div><div>******************* ERROR ENDING ***************</div><div>hpc-cmb(231):</div><div><br></div><br><div class="gmail_quote">
On Tue, Aug 7, 2012 at 10:05 AM, Andreas Förster <span dir="ltr"><<a href="mailto:docandreas@gmail.com" target="_blank">docandreas@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Ian,<br>
<br>
I had a similar issue once. Check that your fragment files start with a line reading<br>
<br>
position: 1 neighbors: 200<br>
<br>
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.<br>
<br>
<br>
<br>
Andreas<div class="im"><br>
<br>
<br>
<br>
On 07/08/2012 5:52, Terwilliger, Thomas C wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Hi Ian,<br>
<br>
I think this part of the error message is the best hint:<br>
<br>
finished reading top 0 0mer fragments from<br>
file/dataFiles/aat000_03_05.<u></u>200_v1_3<br>
<br>
I am guessing there is something odd about the fragment file all right.<br>
You could try supplying this file in one of the tests and see if it<br>
causes the test to fail:<br>
<br>
phenix_regression.wizards.<u></u>test_command_line_rosetta_<u></u>quick test_prerefine<br>
<br>
then:...<br>
<br>
cd test_prerefine<br>
phenix.mr_rosetta seq_file=seq.dat search_models=coords1.pdb<br>
start=place_model stop=place_model data=fobs.mtz is_sub_process=True<br>
already_placed=true refine_after_mr=False run_prerefine=True<br>
number_of_prerefine_models=1 rosetta_fixed_seed=1571<br>
fragment_files=/Users/terwill/<u></u>unix/PHENIX/phenix-dev-894/<u></u>phenix/phenix/rosetta/dummy_<u></u>fragments_file_3.gz<br>
fragment_files=/Users/terwill/<u></u>unix/PHENIX/phenix-dev-894/<u></u>phenix/phenix/rosetta/dummy_<u></u>fragments_file_9.gz<br>
<br>
Then, try above with your fragment files...<br>
<br>
That might point out the problem!<br>
All the best,<br>
Tom T<br>
<br>
<br>
<br>
<br>
<br>
<br></div>
*From:* <a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<u></u>online.org</a><div class="im"><br>
[<a href="mailto:phenixbb-bounces@phenix-online.org" target="_blank">phenixbb-bounces@phenix-<u></u>online.org</a>] on behalf of Ian Slaymaker<br>
[<a href="mailto:slaymake@usc.edu" target="_blank">slaymake@usc.edu</a>]<br></div>
*Sent:* Tuesday, August 07, 2012 10:21 AM<br>
*To:* <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
*Subject:* [phenixbb] mr_rosetta problems<div><div class="h5"><br>
<br>
I am trying to get mr_rosetta working on our cluster and am running into<br>
some problems I am not sure how to solve. The<br>
phenix_regression.wizards.<u></u>test_command_line_rosetta_<u></u>quick_tests tests<br>
went smoothly were completed.<br>
<br>
However, my first test run with all the defaults (not submitted to<br>
multiple processors) using my reflection file, HHR analysis file,<br>
sequence file, and the 2 fragment files failed with the below errors. I<br>
checked all the files, and it seems this is a problem with the fragment<br>
files but I am not sure exactly what they are supposed to look like.<br>
<br>
I thought it could be because our cluster doesnt have access to any<br>
outside networks...is this a problem with rosetta not being able to<br>
download pdb files? if so, is there a way to supply them internally?<br>
The aligned model looks somewhat what I expected it to (same beta sheet<br>
arrangement) but it seems to be incomplete.<br>
Any help would be very much appreciated!<br>
<br>
<br>
<br>
Splitting work into 100 jobs and running with 1 processors using sh<br>
background=None in /MR_ROSETTA_1/GROUP_OF_<u></u>ROSETTA_REBUILD_1/RUN_1/<u></u>REBUILD_IN_SETS_1<br>
<br>
Starting job 1...Log will be: /MR_ROSETTA_1/GROUP_OF_<u></u>ROSETTA_REBUILD_1/RUN_1/<u></u>REBUILD_IN_SETS_1/RUN_FILE_1.<u></u>log<br>
<br>
******************* ERROR ENDING ***************<br>
mr_rosetta failed...<br>
<br>
******************************<u></u>******************************<u></u>********************<br>
Sorry, a subprocess has failed...<br>
<br>
END OF LOG FILE /MR_ROSETTA_1/GROUP_OF_<u></u>ROSETTA_REBUILD_1/RUN_1/<u></u>REBUILD_IN_SETS_1/RUN_FILE_1.<u></u>log :<br>
<br>
to match the actual PDB sequence:<br>
(protein sequence)<br>
New alignment line 4 for PDB:<br>
(protein sequence)<br>
<br>
<br>
Start position of target sequence in sequence file: 0<br>
<br>
Aligned model for comparison: /MR_ROSETTA_1/GROUP_OF_<u></u>ROSETTA_REBUILD_1/RUN_1/<u></u>REBUILD_IN_SETS_1/RUN_1/WORK_<u></u>1/aligned_model.pdb<br>
Log for rebuilding: /MR_ROSETTA_1/GROUP_OF_<u></u>ROSETTA_REBUILD_1/RUN_1/<u></u>REBUILD_IN_SETS_1/RUN_1/WORK_<u></u>1/rebuild.log<br>
<br>
**************ERROR ENDING**********************<br>
Failed to run REBUILD...see log file in /MR_ROSETTA_1/GROUP_OF_<u></u>ROSETTA_REBUILD_1/RUN_1/<u></u>REBUILD_IN_SETS_1/RUN_1/WORK_<u></u>1/rebuild.log<br>
<br>
<br>
The rebuild log had repeats of several errors that I am not sure how to address:<br>
<br>
core.conformation.<u></u>Conformation: [ WARNING ] missing heavyatom: CD2 on residue PHE 3 (repeated several times)<br>
<br>
core.fragments.<u></u>ConstantLengthFragSet: line too short: Skipping line ' (repeated several times)<br>
<br>
<br>
core.fragments.<u></u>ConstantLengthFragSet: finished reading top 0 0mer<br>
fragments from file/dataFiles/aat000_03_05.<u></u>200_v1_3<br>
protocols.loops.loops_main: Frag libraries debug none 1<br>
<br>
<br>
<br>
<br>
<br>
<br></div></div><div class="im">
______________________________<u></u>_________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/<u></u>mailman/listinfo/phenixbb</a><br>
<br>
</div></blockquote><span class="HOEnZb"><font color="#888888">
<br>
-- <br>
Andreas Förster, Research Associate<br>
Paul Freemont & Xiaodong Zhang Labs<br>
Department of Biochemistry, Imperial College London<br>
<a href="http://www.msf.bio.ic.ac.uk" target="_blank">http://www.msf.bio.ic.ac.uk</a></font></span><div class="HOEnZb"><div class="h5"><br>
______________________________<u></u>_________________<br>
phenixbb mailing list<br>
<a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/<u></u>mailman/listinfo/phenixbb</a><br>
</div></div></blockquote></div><br>