The ModelTrimmer application is used to filter models in an existing SEWING model file needs to trim models leaving only relevant models to speed up during 'model comparison' and 'assembly of models'.
ModelTrimmer requires a SEWING model file, which is generated using the SEWING Hasher application as described here. An input PDB file (using -in:file:s) is also required but is not used.
ModelTrimmer outputs a new SEWING model file which has been trimmed using the filters specified in the command-line options.
-in:file:s The input PDB (ignored, but still required)
-sewing:model_file_name The name of the input SEWING model file
-sewing:new_model_file_name The name of the output trimmed model file
-sewing::remove_any_dssp Remove any model that contain this DSSP (H,E,L) (Default "")
-sewing::min_helix_length Remove any model that has less helical residues than this (Default 0)
-sewing::max_helix_length Remove any model that has more helical residues than this (Default 1000)
-sewing::min_strand_length Remove any model that has less strand residues than this (Default 0)
-sewing::max_strand_length Remove any model that has more strand residues than this (Default 1000)
-sewing::min_loop_length Remove any model that has less loop residues than this (Default 0)
-sewing::max_loop_length Remove any model that has more loop residues than this (Default 1000)
-sewing::leave_models_with_E_terminal_ss Remove any model whose two terminal secondary structures are not beta-strands
-sewing::leave_parallel_way_H_bonded_models_by_terminal_strands_only (b-a-b)
-sewing::leave_antiparallel_way_H_bonded_models_by_terminal_strands_only (b-a-b)
-sewing::model_should_have_at_least_one_E Model should have at least one 'E' segment
-sewing::model_should_have_at_least_one_E_at_terminal_segment Model should have at least one 'E' segment at terminal segmentAn example command line for ModelTrimmer:
/path/to/rosetta/main/source/bin/ModelTrimmer.default.linuxgccrelease @flags_ModelTrimmerAn example of flags_ModelTrimmer that would remove all models containing helical segments:
-s input_files/1_1_1TEN_A_res-renum.pdb #just for jd2
-mute basic.io core protocols.jd2
-sewing:model_file_name basic.models
-new_model_file_name basic_trimmed.models
-sewing::remove_any_dssp HModelTrimmer is used to generate input files for the SEWING protocol. More details on its usage can be found on the Model generation page.