Fix format of command lines

[momeara]

• Add short description of what each stage does
• Pull out user specific paths and extensions
• Add line continuation characters so the command lines can be copied and pasted into the terminal
• fix broken paths to input structures
• remove .gz extension from input structures
• add pointer to when and how to run the analysis

  Paths and Extensions

ROSETTA_BASE=<path/to/rosetta>
EXTENSION=linuxgccrelease
WORKING_DIRECTORY=.
BENCHMARK_PATH=<path/to/sequence-tolerance>

Backrub Step

Generate Backrub ensemble for each prototypical conformation. 3-5 minutes per structure. Generates

${WORKING_DIRECTORY}/1N7T_01_0001.pdb
${WORKING_DIRECTORY}/1N7T_01_0001_low.pdb
${WORKING_DIRECTORY}/1N7T_01_0001.pdb

Rosetta 3.2

${ROSETTA_BASE}/rosetta_source/bin/backrub.${EXTENSION} -database ${ROSETTA_BASE}/rosetta_database \
    -s ${BENCHMARK_PATH}/input/pdbs/1N7T_01.pdb -ex1 -ex2 -extrachi_cutoff 0 -mute core.io.pdb.file_data \
    -backrub:ntrials 10000 -score:weights ${BENCHMARK_PATH}/input/backrub_seqtol/rosetta3.2/standard_NO_HB_ENV_DEP.wts \
    -score:patch score12

Rosetta, 2013-08-11 onwards [2]_

${ROSETTA_BASE}/main/source/bin/backrub.${EXTENSION} -database ${ROSETTA_BASE}/main/database \
    -s ${BENCHMARK_PATH}/input/pdbs/1N7T/1N7T_01.pdb -ex1 -ex2 -extrachi_cutoff 0 -mute core.io.pdb.file_data \
    -backrub:ntrials 10000

Sequence tolerance step

Add description of what this does. ~ 20 minutes per generation per structure. Generates

1N7T_01_0001_0001_WETKI.pdb
1N7T_01_0001.ga.entities.gz
1N7T_001.ga.generations.gz

Rosetta 3.2

${ROSETTA_BASE}/rosetta_source/bin/sequence_tolerance.${EXTENSION} -database ${ROSETTA_BASE}/rosetta_database \
    -s ${WORKING_DIRECTORY}/1N7T_01_0001_low.pdb -ex1 -ex2 -extrachi_cutoff 0 -score:ref_offsets HIS 1.2 \
    -seq_tol:fitness_master_weights 1 1 1 2 -ms:generations 5 -ms:pop_size 2000 -ms:pop_from_ss 1 \
    -ms:checkpoint:prefix 1N7T_01_0001 -ms:checkpoint:interval 200 -ms:checkpoint:gz \
    -score:weights ${BENCHMARK_PATH}/input/backrub_seqtol/rosetta3.2/standard_NO_HB_ENV_DEP.wts -out:prefix 1N7T_01_0001 \
    -score:patch score12 -resfile ${BENCHMARK_PATH}/input/backrub_seqtol/1N7T_seqtol.resfile

Rosetta, 2013-08-11 onwards [2]_

${ROSETTA_BASE}/main/source/bin/sequence_tolerance.${EXTENSION} -database ${ROSETTA_BASE}/main/database \
    -s ${WORKING_DIRECTORY}/1N7T_01_0001_low.pdb -ex1 -ex2 -extrachi_cutoff 0 -ex1aro -ex2aro \
    -seq_tol:fitness_master_weights 1 1 1 2 -ms:generations 5 -ms:pop_size 2000 -ms:pop_from_ss 1 \
    -ms:checkpoint:prefix 1N7T_01_0001 -ms:checkpoint:interval 200 -ms:checkpoint:gz \
    -out:prefix 1N7T_01_0001 -resfile ${BENCHMARK_PATH}/input/backrub_seqtol/1N7T_seqtol.resfile

Analysis Step

Run analysis as described in analysis/README.rst

[spiderbaby]

Thanks - the documentaion has been updated.