[phenixbb] MR_Rosetta

Heather Condurso condurso at bc.edu
Fri Jun 15 14:06:11 PDT 2012


The WORK_1 folder only contains "imported_fp_sigfp_freer.mtz".  I ran the regression test this is the result:

~ heather$ /Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/build/mac-intel-osx-x86_64/bin/phenix_regression.wizards.test_command_line_rosetta_quick test_hhr
Skipping phenix rosetta tests: rosetta build not available.
~ heather$ 

The rosetta build is indeed available and I have gotten other MR_rosetta runs to begin as long as I supply my own models.  Also there were a few other regression tests with similar names that I tried as well.  

~ heather$ /Applications/PHENIX-1.8-1069/Contents/phenix-1.8-1069/build/mac-intel-osx-x86_64/bin/phenix_regression.wizards.test_command_line_rosetta ; exit;
Running all command_line tests
Number of tests to run: 7
Running test_mr_rescoring
x coord_mr.1.pdb
x coord_mr.1_data.mtz
x cycle_best_2.mtz
x cycle_best_2_nf.map
x edited_align.ali
x fobs.mtz
x mr_rescoring.eff
x mr_rescoring.pkl
x perfect.mtz
x seq.dat
x test_mr_rescoring.com
x test_mr_rescoring.log
FAILED TO RUN: test_mr_rescoring
Error: test_command_line_rosetta failed

[Process completed]

I don't know what is going on here, but any more ideas are greatly appreciated.


 |  On Fri, 15 Jun 2012 19:29:49 +0000
 |  "Terwilliger, Thomas C" <terwilliger at lanl.gov> wrote:
 |  Hi again Heather,
 |  One other idea:  try this regression test:
 |     phenix_regression.wizards.test_command_line_rosetta_quick test_hhr
 |  It should take a second or two and will say "OK" if everything is all right and it can start from an hhr file.  If that works...then you can look at the commands in 
 |      test_hhr/test_hhr.com
 |  which should look like:
 |    phenix.mr_rosetta data=1dfn.mtz seq_file=1dfn.seq hhr_files=1dfn.hhr number_of_models=1 \
 |  number_of_models_to_skip=2 start_point=place_model stop_point=place_model \
 |   run_place_model=False
 |  and run this command directly, gradually changing all the inputs in it until they match yours...and somewhere along the way it should fail, giving you a clue what needs to be fixed.
 |  All the best,
 |  Tom T
 |  ________________________________________
 |  From: Terwilliger, Thomas C
 |  Sent: Friday, June 15, 2012 1:17 PM
 |  To: PHENIX user mailing list
 |  Cc: Terwilliger, Thomas C
 |  Subject: RE: [phenixbb] MR_Rosetta
 |  Hi Heather,
 |  This should work from an hhr file as you tried to do...I just tried an example to make sure.  I am guessing that something happened in the downloading of the PDB file.  Can you look in your file:
 |     WORK_1/*/mr_model_preparation.log
 |  to see if there is an error listed there?
 |  If that doesn't help, let me know.
 |  All the best,
 |  Tom T
 |  ________________________________________
 |  From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Heather Condurso [condurso at bc.eduSent: Friday, June 15, 2012 12:58 PM
 |  To: phenixbb at phenix-online.org
 |  Subject: [phenixbb] MR_Rosetta
 |  Hello all,
 |  I am working on a structure for which a good molecular replacement model doesn't really exist ( highest sequence similarity is 24% for a protein with completely different function and even worse for proteins with a more similar function).  As I try and solve the phase with Se-Met derived protein, I thought I would try and use MR_rosetta and see what happens.   I have also tried to use pyrosetta to generate better models, but the structure alignments suggest my protein to be primarily composed of beta sheets so the models from ab initio methods aren't great.  I am using the GUI and have given my sca file, a sequence file, the 3 and 9 fragment files, and both the global and local alignment hhr files.  I thought that phenix would use the hhr alignments to pull models directly from the pdb, but without giving a model pdb, MR_rosetta fails.  So my question is how do I input the models?  Should I download each of the pdbs and clean them up a bit?  How many should I include? I !
 |   rstand the more I include the more computing time this will take.  Can you give any recommendations as to other parameters to change keep the computing time down initially to identify the best model before extensive time is used?
 |  I appreciate any help you may be able to provide,
 |  Heather Condurso
 |  UF-Department of Chemistry
 |  condurso at ufl.edu
 |  _______________________________________________
 |  phenixbb mailing list
 |  phenixbb at phenix-online.org
 |  http://phenix-online.org/mailman/listinfo/phenixbb

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