Command lines for Comparative Modeling Tutorial
Rosetta Workshop, March 2011
Elizabeth Dong

COMMAND FOR COMPARATIVE MODELING PROTOCOL:

$ROSETTA_BIN/minirosetta.$ROSETTA_SUFFIX @$WORKSHOP_ROOT/tutorials/modeling/input_model/comparative_model.options -database $ROSETTA_DATABASE >& $WORKSHOP_ROOT/tutorials/modeling/output_model/comparative_model.log &

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COMMANDS FOR LOOP BUILDING PROTOCOL:

REMOVE LOOP COORDINATES

$WORKSHOP_ROOT/py_protein_utils/scripts/remove_loop_coords.py 2foxA.loops 2foxA_start_model.pdb 2foxA_no_loops.pdb

CCD

$ROSETTA_BIN/loopmodel.$ROSETTA_SUFFIX @$WORKSHOP_ROOT/tutorials/modeling/input_loop/ccd.options -database $ROSETTA_DATABASE >& $WORKSHOP_ROOT/tutorials/modeling/output_loop/ccd.log &

KIC

$ROSETTA_BIN/loopmodel.$ROSETTA_SUFFIX @$WORKSHOP_ROOT/tutorials/modeling/input_loop/kic.options -database $ROSETTA_DATABASE >& $WORKSHOP_ROOT/tutorials/modeling/output_loop/kic.log &

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COMMAND FOR CLUSTERING PROTOCOL:



CLUSTERING SCRIPT



python $WORKSHOP_ROOT/py_protein_utils/scripts/clustering.py --silent=cluster_all.out --rosetta=$ROSETTA_BIN/cluster.$ROSETTA_SUFFIX --database=$ROSETTA_DATABASE --options=cluster.options cluster_summary.txt cluster_histogram.txt



EXTRACTING PDB FILES



$ROSETTA_BIN/score_jd2.$ROSETTA_SUFFIX -database $ROSETTA_DATABASE -in:file:silent $WORKSHOP_ROOT/tutorials/modeling/input_cluster/cluster_all.out -in:file:silent_struct_type binary -out:output -out:pdb -out:file:fullatom -in:file:tags S_1F4PA_0410_1 S_1F4PA_0356_1 S_1F4PA_0036 S_1F4PA_0281 S_1F4PA_0127_1 S_1F4PA_0116_1
