scripting_documentation/RosettaScripts/Movers/SpliceIn

Table of Contents

Author

Gideon Lapidoth; glapidoth@gmail.com; PI: Sarel J. Fleishman; sarel@weizmann.ac.il

Overview

Brief

This mover is used to apply the phi, psi, and omega torsion angles from a pre-computed torsion database (see SpliceOut). onto the corresponding segment of the pose. The template PDB is used to correspond between the torsion database and current pose, therefore the template PDB and pose need to be aligned. The same template pdb used to build the torsion database should be used here.

<SpliceIn name="(&string;)" tolerance="(0.23 &real;)"
        ignore_chain_break="(false &bool;)" debug="(false &bool;)"
        min_seg="(false &bool;)" CG_const="(false &bool;)"
        rb_sensitive="(false &bool;)" chain_num="(1 &non_negative_integer;)"
        superimposed="(true &bool;)"
        source_pdb_to_res="(&refpose_enabled_residue_number;)"
        skip_alignment="(false &bool;)" use_sequence_profile="(&bool;)"
        scorefxn="(&string;)" template_file="(&string;)"
        task_operations="(&task_operation_comma_separated_list;)"
        design_task_operations="(&string;)" residue_numbers_setter="(&string;)"
        torsion_database="(&string;)" database_entry="(&non_negative_integer;)"
        database_pdb_entry="(&string;)" design_shell="(6.0 &real;)"
        repack_shell="(8.0 &real;)" randomize_cut="(false &bool;)"
        cut_secondarystruc="(false &bool;)" delta_lengths="(&int_cslist;)"
        thread_original_sequence="(false &bool;)" rtmin="(true &bool;)"
        dbase_iterate="(false &bool;)" checkpointing_file="(&string;)" >
    <Segments name="(&string;)" profile_weight_away_from_interface="(1.0 &real;)"
            current_segment="(&string;)" >
        <segment name="(&string;)" pdb_profile_match="(&string;)" profiles="(&string;)" />
    </Segments>
</SpliceIn>

tolerance: tolernace of bond length std when checking for chain breaks
ignore_chain_break: if there is a chain break don't fail
debug: more verbose during run
min_seg: minimize segment after splice in?
CG_const: apply coordinate constraints on C-gamma atoms
rb_sensitive: apply rigid body addaptations
chain_num: which chain number to apply splice on
segment: segment name
superimposed: are thr structures superimposed
delete_hairpin: delete hairpin segment?
delete_hairpin_n: how many residues to delete on N-ter hairpin
delete_hairpin_c: how many residues to delete on C-ter hairpin
tail_segment: what direction is the tail segment
source_pdb_to_res: residue number of last residue on source segment
skip_alignment: whether to align pose to source pdb
use_sequence_profile: Use sequence profiles in design?
scorefxn: Name of score function to use
template_file: What is the template file to use during design
task_operations: A comma separated list of TaskOperations to use.
design_task_operations: XRW TO DO
residue_numbers_setter: XRW TO DO
torsion_database: torsion db file name
database_entry: choose db entry by number
database_pdb_entry: XRW TO DO
design_shell: design shell radius
repack_shell: packing shell radius
randomize_cut: should the cut be put randomly in the designed segment
cut_secondarystruc: put cut into ss
delta_lengths: comma separated list of allowed segment delta lengths
thread_original_sequence: thread sequence from source pdb onto design
rtmin: should we apply rtmin after design
dbase_iterate: should we iterate through the db file
checkpointing_file: name of checkpointing file

Subtag Segments: Wrapper for multiple segments tags

profile_weight_away_from_interface: XRW TO DO
current_segment: XRW TO DO

Subtag segment: individual segment tag

pdb_profile_match: XRW TO DO
profiles: XRW TO DO

Example

Currently, this mover is only accessible via RosettaScripts. The new segment's conformation will be stored in test.db file. The mover "min" is used to optimize the new backbone conformation in the context of the pose.

An example RosettaScripts tag is below:

			<SpliceOut name="spliceout" source_pdb="source.pdb" torsion_database="test.db" scorefxn="talaris14" randomize_cut="1" cut_secondarystruc="0" from_res="127" to_res="199" rms_cutoff="0.25" design_shell="0.01" repack_shell="0.01" splice_filter="chainbreak_val" template_file="template.pdb" task_operations="init,rtr" debug="0" mover="min" superimposed="1"> 
 <Segments current_segment="blade4"/>
</SpliceOut>