Rosetta 3.1 Release Manual

Extra Command Lines

We list a few more sample command lines which are using our release applications.

• scoring:

  ./rosetta_source/bin/score.linuxgccrelease  -database ~/rosetta_database/ -score:weights score13_env_hb -in:file:s testt0389_refinement_start1_0001.pdb
  

• backrub:

  ./backrub.linuxgccrelease -s my.pdb -ex1 -ex2aro -ex1aro -backrub:pivot_residues 10 11 12 13 14 15 -packing:resfile Resfile -backrub:ntrials 5000 -backrub:mc_kt 1.0 -database ~/rosetta_database/ -out:nstruct 1000
  

• relax:

  ./relax.linuxgccrelease -database ~/rosetta_database/  -score:weights score13_env_hb -out:pdb -out:prefix relaxed -out:nstruct 100 -in:file:s my.pdb 

• relax with constraints:

  ./relax.linuxgccrelease -database ~/rosetta_database/  -score:weights score13_env_hb -out:pdb -out:prefix constrained -constraints:cst_fa_file constraints_file -constraints:cst_fa_weight 2.0 -out:nstruct 100 -in:file:s my.pdb
  

• loop modeling with constraints:

  add -constraints:cst_fa_file and -constraints:cst_fa_weight
  cst_weight can be higher (up to 10, even 100)
  

  sample constraints file:

  AtomPair CZ 64 CA 8 GAUSSIANFUNC 6.39 2.0
  

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