Command lines collection for pilot/public applications

Metadata

This document was edited Nov 10th 2008 by Yi Liu. Credits go to developers who helped me to collect these useful command lines.

Instructions

• There is no specific examples for every pilot applications in the rosetta trunk yet.
• Make sure that you have the application in the pilot_apps.src.settings.
• Or, you can build all pilot applications with the scons flag pilot_apps_all

Command lines collected from Firas

Please read the options list to find the descriptions for each option in the commands

• backrub:

  path/to/rosetta/rosetta_source/bin/backrub.linuxgccrelease -s 1cc8_model15.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 path/to/rosetta/rosetta_database/ -out:nstruct 1000
  

• scoring with rosetta:

  path/to/rosetta/rosetta_source/bin/backrub.linuxgccrelease -s 1cc8_model15.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 path/to/rosetta/rosetta_database/ -out:nstruct 1000
  

• scoring with rosetta:

  path/to/rosetta/rosetta_source/bin/backrub.linuxgccrelease -s 1cc8_model15.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 path/to/rosetta/rosetta_database/ -out:nstruct 1000
  

• relax with rosetta:

  path/to/rosetta/rosetta_source/bin/relax.linuxgccrelease -database /path/to/rosetta/rosetta_database/  -score:weights score13_env_hb -out:pdb -out:prefix relaxed -out:nstruct 100 -in:file:s 1utg_model39.pdb 
  

• relax with constraints in rosetta:

  /path/to/rosetta/rosetta_source/bin/relax.linuxgccrelease -database path/to/rosetta/rosetta_database/  -score:weights score13_env_hb -out:pdb -out:prefix constrained -constraints:cst_file constraints_file -constraints:cst_weight 2.0 -out:nstruct 100 -in:file:s 1utg_model39f.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
  

• make a loop

  path/to/rosetta/rosetta_source/bin/minirosetta.linuxgccrelease @args
  

  with args file:

  -in::file::s  threaded-model.pdb
  -database /path/to/rosetta/rosetta_database/
  -loops::frag_sizes 9 3 1
  -loops::frag_files aat000_09_05.200_v1_3 aat000_03_05.200_v1_3 none
  -loops::loop_file t000_.loopfile
  -score:weights score13_env_hb
  -psipred_ss2 fragments/t000_.psipred_ss2
  -run::protocol looprelax
  -loops::remodel quick_ccd
  -loops::relax fullrelax
  -out::nstruct 100
  -in:file:fullatom
  -out::pdb
  -out::prefix lr_decoys
  

• packstate:

  /path/to/rosetta/rosetta_source/bin/packstat.linuxgccrelease -database /path/to/rosetta/rosetta_database -packstat:packstat_pdb -s 1shf.pdb
  

Command lines collected from Steven Lewis

Please read the options list to find the descriptions for each option in the commands

• options file for pilot/rjha/MatchFilter.cc

  -database /path/to/rosetta/rosetta_database
  -options::user
  -run::version
  -mute core
  -l pdblist
  

• options file for pilot/rjha/MetalInterfaceStructureCreator.cc

  -database /path/to/rosetta/rosetta_database
  -s NE2.pdb
  -run::version
  -options::user
  -resfile resfile
  

• options file for pilot/rjha/MetalInterfaceStructureCreator.cc

  -database /path/to/rosetta/rosetta_database
  -s NE2.pdb
  -run::version
  -options::user
  -resfile resfile
  -ex1
  -ex2
  -extrachi_cutoff 1
  -use_input_sc
  -run::min_type dfpmin_armijo_nonmonotone
  -nstruct 1
  -AnchoredDesign::perturb_temp 1.0
  -AnchoredDesign::perturb_cycles 500
  -AnchoredDesign::perturb_show
  -AnchoredDesign::refine_cycles 1
  -pose_metrics::interface_cutoff 10
  local options:
  -MetalInterface::partner1 (partner 1, defaults to ank.pdb)
  -MetalInterface::partner2 (partner 2, defaults to ubc12.pdb)
  -MetalInterface::partner2_residue (which residue on ubc12 to replace,defaults to 62)
  -skip_sitegraft_repack
  

• options file for pilot/smlewis/AnchoredDesign.cc

  -database /path/to/rosetta/rosetta_database
  -mute core.chemical core.scoring.etable core.io.database
  core.io.pdb.file_data core.conformation core.pack.pack_rotamers
  core.pack.task
  -run::version
  -options::user
  -s /netscr/smlewis/18_1F11_design_132cut/1F11_t-1QWF.pdb
  -loops::loop_file loopsfile
  -in::file::frag3/netscr/smlewis/18_1F11_design_132cut/aat000_03_05.200_v1_3.plusSH3.gz
  -resfile /netscr/smlewis/18_1F11_design_132cut/resfile/netscr/smlewis/18_1F11_design_132cut/resfile2
  -ex1
  -ex2 #only later
  -use_input_sc
  -run::min_type dfpmin_armijo_nonmonotone
  -AnchoredDesign::anchor /netscr/smlewis/18_1F11_design_132cut/anchor
  -AnchoredDesign::debug
  -AnchoredDesign::refine_only
  -AnchoredDesign::perturb_show
  -AnchoredDesign::perturb_report 1
  -AnchoredDesign::perturb_temp
  -AnchoredDesign::refine_report 1
  -AnchoredDesign::refine_temp
  -AnchoredDesign::refine_repack_cycles 30
  -constant_seed
  -jran !!!
  -AnchoredDesign::perturb_cycles 300
  -AnchoredDesign::refine_cycles 1000
  -nstruct 334
  

Command lines collected from Ben Stranges

• Sarel's dock_design_parser

  -database ../database  (path to database)
  -s pdbname.pdb  (structure to dock/design)
  -parser:protocol protocol_name.protocol  (the file that contains the XML formatted protocol to use)
  -parser:ntrials 10  (number of total times the parser is run)
  -nstruct 5  (total number of possible structures (pdbs) output)
  -parser:view  (gives graphics of protocol; need to compile with extras=graphics for this to work)