[phenixbb] MR_Rosetta prerefine question

Terwilliger, Thomas C terwilliger at lanl.gov
Fri Nov 8 10:26:15 PST 2013

Hi Heather,

That would be useful, I can see that. I don't think there is an easy way to do that in mr_rosetta.   There are two possibilities I can think of.

1. You can pass any Rosetta commands you want to mr_rosetta with the keyword "rosetta_command".  I will ask Frank Dimaio from the Baker group about what commands might do this.

2. Alternatively you could fix it up by hand afterwards by using the phenix model tools to select some residues from the original model and some residues from the new model and then just make a composite PDB file.

All the best,
Tom T

On Nov 8, 2013, at 11:02 AM, Heather L Condurso wrote:

Dear all,

I am trying to use the rosetta prerefinement fuction of MR_rosetta to complete a homology model with missing stretches of amino acids.  Everything runs fine and residues are being added to fill the gaps using the fragment files, but rosetta is also altering parts of the model which should already be well placed.  Is there a way to tell Rosetta only to prerefine certain residues?

I've been following the command line suggestion:

phenix.mr_rosetta \
  seq_file=seq.dat \
  data=coords1.mtz \
  search_models=coords1.pdb \
  run_prerefine=True \
  number_of_prerefine_models=1000 \
  fragment_files = test3.gz \
  fragment_files = test9.gz \
  rescore_mr.relax=False \
  rosetta_models=100 \
  ncs_copies=2 \
  space_group=p212121  \
  use_all_plausible_sg=False \
  nproc=200 \

Heather Condurso
condurso at bc.edu<mailto:condurso at bc.edu>
phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>

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