[phenixbb] MR_Rosetta prerefine question

[Heather L Condurso]

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 \
  group_run_command=qsub


Thanks,
Heather Condurso
condurso at bc.edu
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