rosetta

command

~/rosetta/bin/pdb_to_map.default.linuxgccrelease -in:file:s 4d0m_tetramer.pdb.clean.pdb -edensity:mapreso 10.0 -edensity:grid_spacing 2.0 -in:file:centroid_input  -mapfile 4d0m_tetramer.map

hhblits -o /dev/null -i 1v0eA_frag.fasta -oa3m 1v0eA_frag.a3m -d /lab/databases/hhsuite/uniprot/un    iprot20_2013_03/uniprot20_2013_03 -cpu 20

hhblits -o /dev/null -i to_threadon_1v0eA_frag.fasta -oa3m to_threadon_1v0eA_frag.a3m -d /lab/data       bases/hhsuite/uniprot/uniprot20_2013_03/uniprot20_2013_03 -cpu 20

hhalign -i to_threadon_1v0eA_frag.a3m -t 1v0eA_frag.a3m  -glob -o to_threadon_1v0eA_frag.hha

~krypton/scripts/hhs2partial_thread.pl -hhs to_threadon_1v0eA_frag.hha -fas 1v0eA_frag.fasta -name        1v0eA_1

~wangyr/cm_scripts/bin/convert_aln.pl  to_threadon_1v0eA_frag.hha -format_in hhsearch -format_out        grishin > to_threadon_1v0eA_frag.alt

fold and dock

-run:protocol broker

-broker:setup [topology file]
-file:frag3 [3mer fragments file]
-file:frag9 [9mer fragments file]
-in:file:fasta [fasta sequence file] -symmetry:symmetry_definition [symmetry definition file] -relax:fast

-relax:jump_move -symmetry:initialize_rigid_body_dofs -fold_and_dock::rotate_anchor_to_x -rg_reweight 0.001 -abinitio:increase_cycles 0.2 -rigid_body_cycles 1 -abinitio:recover_low_in_stages 0

-rigid_body_frequency 0.2 

-rigid_body_disable_mc -run:reinitialize_mover_for_each_job 

-score:weights score12_full

-nstruct [number of docking calculations for each input monomer] -out:file:silent [output structure file in silent format] 

###################################
[topology file]
CLAIMER FoldandDockClaimer
END_CLAIMER


###################################
#a minimal setup
-run:protocol broker
-broker:setup setup_init.tpb
-database minirosetta_database

-nstruct 200
-out:file:silent_struct_type binary

-in:file:fasta t000_.fasta
-file:frag3 t000_.200.3mers
-file:frag9 t000_.200.9mers

-rg_reweight 0.001
-run:reinitialize_mover_for_each_job

-score:find_neighbors_3dgrid

-symmetry:symmetry_definition D2.symm
-symmetry:initialize_rigid_body_dofs
-fold_and_dock::rotate_anchor_to_x

-relax:fast
-relax:jump_move

foldit

Here is a very bare-bones cheat sheet:

To load a PDB, enter into any puzzle in the game, then press
CTRL+ALT+SHIFT+A to load a protein, CTRL+ALT+SHIFT+S to save.

To use DSSP to assign secondary structure: CTRL+ALT+SHIFT+D

How do we see CPK view, CPK + Hydrogen view, active site view?
=> Use following hotkeys
1) CPK view -> press CTRL + SHIFT + C
2) CPK + Hydrogen view -> press CTRL + SHIFT + V
3) Active site view -> press CTRL + SHIFT + X

gdtmm

//write gdtmm to output
#include <core/sequence/util.hh>
core::sequence::SequenceAlignmentOP native_aln;
get_gdtmm
if (native_ && native_->total_residue()) {
	gdtmm = get_gdtmm(*native_, pose, native_aln);
	core::pose::setPoseExtraScore( pose, "GDTMM_after_stage1", gdtmm);
	TR << "GDTMM_after_stage1" << F(8,3,gdtmm) << std::endl;
}

core::Real get_gdtmm( core::pose::Pose & native, core::pose::Pose & pose, core::sequence::SequenceAlignmentOP & aln ) {
	runtime_assert( native.total_residue() > 0 && pose.total_residue() > 0 );
	if ( !aln ) {
		core::sequence::SequenceOP model_seq( new core::sequence::Sequence( pose.sequence(),  "model",  1 ) );
		core::sequence::SequenceOP native_seq( new core::sequence::Sequence( native.sequence(), "native", 1 ) );
		aln = core::sequence::SequenceAlignmentOP( new core::sequence::SequenceAlignment );
		*aln = align_naive(model_seq,native_seq);
	}

	int n_atoms;
	ObjexxFCL::FArray2D< core::Real > p1a, p2a;
	protocols::comparative_modeling::gather_coords( pose, native, *aln, n_atoms, p1a, p2a );

	core::Real m_1_1, m_2_2, m_3_3, m_4_3, m_7_4;
	return core::scoring::xyz_gdtmm( p1a, p2a, m_1_1, m_2_2, m_3_3, m_4_3, m_7_4 );
}

multi-chain hybrid

>fasta: #add "/"
seqA/seqB

-crystal_refine

options

   -constraints:cst_fa_file  <filename>      Add constraints from the fullatom constraint file(*)
   -constraints:cst_fa_weight <weight>       Weight to be used for the constraints in the cst_fa_file.
   -constraints:cst_file  <filename>         Add constraints from the constraint file(*)
   -constraints:cst_weight   <weight>        Weight to be used for the constraints in the cst_file.
   -relax:constrain_relax_to_start_coords    Add coordinate constraints to backbone heavy atoms, based on the input structure.
   -relax:constrain_relax_to_native_coords   Add coordinate constraints to backbone heavy atoms, based on the structure passed to -in:file:native.
   -relax:coord_constrain_sidechains         Also add coordinate constraints to sidechain heavy atoms (requires one of previous two options)
   -relax:coord_cst_stdev    <stdev>         Set the strength of coordinate constraints (smaller=tighter)
   
   -show_simulation_in_pymol X, where X is how many seconds pass between PyMOL updates. 5 is default; low values may overload your computer.
   run /path/to/rosetta/src/python/bindings/PyMOLPyRosettaServer.py (in pymol)
   
   # reduce memory footprint
-chemical:exclude_patches LowerDNA  UpperDNA Cterm_amidation SpecialRotamer  VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated  tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated  lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm

relax

relax.linuxgccrelease -s file.pdb -relax:cartesian -default_max_cycles 200 -default_repeats 1 -score:weights talaris2013_cart

relax.linuxgccrelease -database rosetta/rosetta_database [-extra_res_fa your_ligand.params] -relax:constrain_relax_to_start_coords -relax:coord_constrain_sidechains -relax:ramp_constraints false -s your_structure.pdb

The flags file can contain whatever packing and scorefunction flags you wish to use. We recommend at least:

-ex1
-ex2
-use_input_sc
-flip_HNQ
-no_optH false

https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d9/d2e/prepare_pdb_for_rosetta_with_relax.html

https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/dd/da1/preparing_structures.html

https://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d6/d41/relax_commands.html

rosetta

#compile debug
./scons.py             #exe
./scons.py cat=test    #unit test
python test/run.py -d ~/rosetta/Rosetta/main/database/ --mute all -j20 #run unit test
cd build/test/debug/linux/2.6/64/x86/gcc/4.4/default/
./core.test CenRotModelEnergyTests -database ~/rosetta/Rosetta-cenrot/database/

#compile release
./scons.py mode=release -j20
cd ../test/integeration
./integration.py -d ~/rosetta/Rosetta/main/database/ -j20  #--extras=boost_thread

#cmake
cd build_clang
cmake -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_C_COMPILER=clang .

#compile mpi version on hyak
1. In Rosetta:
source/tools/build/user.settings - you want to uncomment "import os" and uncomment ""program_path"  : os.environ["PATH"].split(":") 

2: In your bashrc load:
module load gcc_4.4.7-ompi_1.6.5

3: Log onto an interactive node:
step1: log onto hyak;
step2: qsub -q int -I -l walltime=5:00:00  

4: compile:
scons -j 8 mode=release extras=mpi rosetta_scripts #--nover

5: Setup your job to use mpi
/work/brunette/hyak_submit_mpi

Goodluck!