[phenixbb] MR_Rosetta prerefine

Terwilliger, Thomas C terwilliger at lanl.gov
Mon Nov 26 11:54:30 PST 2012

Hi Heather,

I have changed mr_rosetta to generate a unique file name for PDB files.  The file name will contain the solution ID to make it unique (here the ID=2003 and the original file name was coords1.pdb):


  Starting with the next overnight build this should be available.  You can turn this on and off with "add_id=True" "add_id=False" if you want (default will be True).

I didn't answer your other question before.  There isn't a place with all the scores during the time that rosetta models are generated, I'm afraid.  You can get them when it finishes the model generation with:

   phenix.mr_rosetta display_solutions=true mr_rosetta-solutions= place_model_results.pkl

All the best,
Tom T

From: Terwilliger, Thomas C
Sent: Thursday, November 01, 2012 8:50 AM
To: PHENIX user mailing list
Cc: Terwilliger, Thomas C
Subject: RE: [phenixbb] MR_Rosetta prerefine

Hi Heather,

Good point. No, at present you can't automatically name these files.  I will change that so that they have unique numbers.

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.edu]
Sent: Thursday, November 01, 2012 8:46 AM
To: phenixbb at phenix-online.org
Subject: [phenixbb] MR_Rosetta prerefine

Dear all,

I am using mr_rosetta to run prerefinement of various starting models that all have pretty low sequence homology to my protein of interest (~15%).  I ran it using the simple script from the manual:

phenix.mr_rosetta \
  seq_file=seq.dat \
  search_models=coords1.pdb \
  run_prerefine=True \

Its working fairly well, but obviously taking a long time to make 1000 models.  Is there a log or score file somewhere that lists all of the rosetta scores as it is running?  Right now all the pdb files in each different run have the format S_"original model name"__0001.pdb no matter what run it resulted from.  Is there a way to make it unique for example with the actual run number in place of 0001?  This makes it difficult to compare files in pymol.

Heather Condurso
UF-Department of Chemistry
condurso at ufl.edu
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