You are here

change number of output pose files written out (default=50) in ligand docking XML script

3 posts / 0 new
Last post
change number of output pose files written out (default=50) in ligand docking XML script

Using the Rosetta docking tutorial XML script as a reference, see below, how can the number of output pose files be changed? It seems there is a default of 50 files set somewhere but unfortunately I cannot find where to overwrite it and can't seem to find any references to it online. I suspect there is a trivial answer to this and I'm just missing the obvious.

There is a MultipleOutputWrapper tag with a max_output_poses attribute but that tag seems to be intended for taking a previously generated pose and using it to generate additional poses. I'm sure there are also filters, etc. that can be used but it seems like there should be an attribute somewhere to change the 50 to a different value.




Rosetta docking script from tutorial:


            <ScoreFunction name="ligand_soft_rep" weights="ligand_soft_rep">
            <ScoreFunction name="hard_rep" weights="ligand">

            <LigandArea name="inhibitor_dock_sc" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
            <LigandArea name="inhibitor_final_sc" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="false"/>
            <LigandArea name="inhibitor_final_bb" chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>

            <InterfaceBuilder name="side_chain_for_docking" ligand_areas="inhibitor_dock_sc"/>
            <InterfaceBuilder name="side_chain_for_final" ligand_areas="inhibitor_final_sc"/>
            <InterfaceBuilder name="backbone" ligand_areas="inhibitor_final_bb" extension_window="3"/>

            <MoveMapBuilder name="docking" sc_interface="side_chain_for_docking" minimize_water="false"/>
            <MoveMapBuilder name="final" sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="false"/>

        <SCORINGGRIDS ligand_chain="X" width="15">
            <ClassicGrid grid_name="classic" weight="1.0"/>

            <Transform name="transform" chain="X" box_size="7.0" move_distance="0.2" angle="20" cycles="500" repeats="1" temperature="5"/>
            <HighResDocker name="high_res_docker" cycles="6" repack_every_Nth="3" scorefxn="ligand_soft_rep" movemap_builder="docking"/>
            <FinalMinimizer name="final" scorefxn="hard_rep" movemap_builder="final"/>
            <InterfaceScoreCalculator name="add_scores" chains="X" scorefxn="hard_rep" native="crystal_complex.pdb"/> 

            <Add mover_name="transform"/>
            <Add mover_name="high_res_docker"/>
            <Add mover_name="final"/>
            <Add mover_name="add_scores"/>


Post Situation: 
Fri, 2019-10-18 13:50

The number of output structures isn't set in the XML itself. Instead, the number of output structures is controlled by the `-nstruct` flag on the command line or in the options file.

(A large number of Rosetta protocols, including the ligand docking protocol here, are "trivially parallel", in the sense that each output structure is independent of any of the others. As such, the XML itself just represents a single pass to make a single output structure. The generation of multiple output structures is controlled at a "higher" level, by running through the XML-represented proceedure multiple times, once per output.)

Fri, 2019-10-18 15:30

Thanks, that's just what I was looking for.

Fri, 2019-10-18 17:16