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 are 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/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/main/database/ -out:nstruct 1000

scoring with rosetta:

path/to/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/main/database/ -out:nstruct 1000

scoring with rosetta:

path/to/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/main/database/ -out:nstruct 1000

relax with rosetta:

path/to/rosetta/source/bin/relax.linuxgccrelease -database /path/to/rosetta/main/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/source/bin/relax.linuxgccrelease -database path/to/rosetta/main/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/source/bin/minirosetta.linuxgccrelease @args

with args file:

-in::file::s  threaded-model.pdb
-database /path/to/rosetta/main/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/source/bin/packstat.linuxgccrelease -database /path/to/rosetta/main/database -packstat:packstat_pdb -s 1shf.pdb

Command lines collected from Steven Lewis

The following are example flags files. The associated applications are deprecated, documented elsewhere, or are not available for public use; these are intended only as generic examples.

options file for pilot/rjha/MatchFilter.cc

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

options file for pilot/rjha/MetalInterfaceStructureCreator.cc

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

options file for pilot/rjha/MetalInterfaceStructureCreator.cc

-database /path/to/rosetta/main/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/main/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)