[phenixbb] MR_Rosetta

Terwilliger, Thomas C terwilliger at lanl.gov
Fri Jun 15 12:29:49 PDT 2012

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 


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 \

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:


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 unde!
 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

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