Command lines for Comparative Modeling Tutorial
Rosetta Workshop, November 2013
Gregory Sliwoski

COMMANDS FOR COMPARATIVE MODELING WITH LOOP BUILDING:

CLEAN PDB
~/rosetta_workshop/Rosetta/tools/protein_tools/scripts/clean_pdb.py 2RH1_noT4L.pdb A

THREAD TARGET SEQUENCE ON TEMPLATE PDB
python2.7 ~/rosetta_workshop/Rosetta/tools/protein_tools/scripts/thread_pdb_from_alignment.py --template=2rh1A --target=1u19A --chain=A --align_format=clustal 1u19A.2rh1A.aln 2rh1A.pdb 1u19A_on_2rh1A.pdb

python2.7 ~/rosetta_workshop/Rosetta/tools/protein_tools/scripts/get_fasta_from_pdb.py 1u19A_on_2rh1A.pdb A 1u19A_on_2rh1A.fasta

1F. OCTOPUS TO SPAN FILE
~/rosetta-3.5/rosetta_source/src/apps/public/membrane_abinitio/octopus2span.pl 1u19A.octopus

2. RUN CCD
~/rosetta_workshop/Rosetta/main/source/bin/loopmodel.default.linuxgccrelease @ccd.options -database ~/rosetta_workshop/Rosetta/main/database >& ccd.log &

3. EXTRACT PDBS FROM SILENT FILE
~/rosetta_workshop/Rosetta/main/source/bin/score_jd2.default.linuxgccrelease -database ~/rosetta_workshop/Rosetta/main/database -in:file:silent 1u19A_on_2rh1A_ccd_test_01.out -score:weights membrane_highres_Menv_smooth.wts -in:file:fullatom -in:file:spanfile 1u19A.span -out:pdb

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COMMAND FOR CLUSTERING PROTOCOL:

CLUSTERING SCRIPT
~/rosetta_workshop/Rosetta/tools/protein_tools/scripts/clustering.py --silent=1u19A_on_2rh1A_ccd_production_01.out --rosetta=/usr/people/molgraph/rosetta_workshop/Rosetta/main/source/bin/cluster.default.linuxgccrelease --database=/usr/people/molgraph/rosetta_workshop/Rosetta/main/database --options=cluster.options cluster_summary.txt cluster_histogram.txt

SORT CLUSTERS BY SIZE
sort –rnk4  cluster_summary.txt > cluster_summary_sorted.txt
head –n 5 cluster_summary_sorted.txt

EXTRACTING PDB FILES
~/rosetta_workshop/Rosetta/main/source/bin/score_jd2.default.linuxgccrelease -database ~/rosetta_workshop/Rosetta/main/database -in:file:silent 1u19A_on_2rh1A_ccd_production_01.out -in:file:silent_struct_type binary -in:file:fullatom -score:weights membrane_highres_Menv_smooth.wts -in:file:spanfile 1u19A.span -out:output -out:pdb -out:file:fullatom -in:file:tags 1u19A_on_2rh1A_ccdS_0241 1u19A_on_2rh1A_ccdS_0310 1u19A_on_2rh1A_ccdS_0394 1u19A_on_2rh1A_ccdS_0028 1u19A_on_2rh1A_ccdS_0286
