[phenixbb] MR_Rosetta prerefine question

[Heather L Condurso]

Tom,

Thanks for the quick reply I will try #2 and see if that gives me a
reasonable model.  If you hear from the Baker lab with a useful command
please let me know.

Thanks again,
~Heather


On Fri, Nov 8, 2013 at 1:26 PM, Terwilliger, Thomas C
<terwilliger at lanl.gov>wrote:

>  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 \
>   group_run_command=qsub
>
>
>  Thanks,
>  Heather Condurso
>  condurso at bc.edu
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