[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):
coords1_S_COORD_0001_su_2003_ed.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 \
number_of_prerefine_models=1000
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.
Thanks,
Heather Condurso
UF-Department of Chemistry
condurso at ufl.edu
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