RemoveMetalConnectionsMover

Documentation and mover by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org). Documentation added on Remembrance Day 2020.

Table of Contents

- RemoveMetalConnectionsMover

Description

This mover complements the function of the -in:auto_setup_metals command line flag or the SetupMetalsMover by providing a means of removing the automatically-added bonds between metals and metal-liganding residues and of removing the corresponding variant types. Note that, at the present time, this mover does not remove metal constraints. Those must be removed using the ClearConstraintsMover.

Setup and options

Autogenerated Tag Syntax Documentation:

A mover that removes bonds between metals and metal-liganding atoms that were added with the SetupMetalsMover or with the -auto_setup_metals commandline flag. This mover also reverts the metal residue and the metal-liganding residue back to the types that lack the extra bonds. Note that at the present time it does not remove metal constraints.

References and author information for the RemoveMetalConnectionsMover mover:

RemoveMetalConnectionsMover Mover's author(s): Vikram K. Mulligan, Center for Computational Biology, Flatiron Institute vmulligan@flatironinstitute.org

<RemoveMetalConnectionsMover name="(&string;)" residue_selector="(&string;)" />

residue_selector: A residue selector for selecting those residues from which to remove metal bonds and variant types. If a residue AND the metal that it binds are both selected, bonds and variant types are removed from both. The mover applies to the whole pose if no residue selector is provided. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.

Example

The following script applies metal-binding constraints to the input pose, then relaxes it using the FastRelax mover, then removes metal constraints, introduces a mutation, adds back metal constraints, and relaxes again:

<ROSETTASCRIPTS>
        <SCOREFXNS>
                <ScoreFunction name="r15_cst" weights="ref2015_cst.wts" >
                        <Reweight scoretype="metalbinding_constraint" weight="1.0" />
                </ScoreFunction>
        </SCOREFXNS>
        <MOVERS>
                <SetupMetalsMover name="setup_metals" metals_detection_LJ_multiplier="1.0" />
                <FastRelax name="frlx1" scorefxn="r15_cst" />
		<RemoveMetalConnectionsMover name="remove_metal_bonds" />
		<ClearConstraintsMover name="clear_csts" />
		<MutateResidue name="introduce_mutation" target="63" new_res="ALA" /> #We suppose that residue 63 was a metal-binding residue. 
        </MOVERS>
        <PROTOCOLS>
                <Add mover="setup_metals" />
                <Add mover="frlx1" />
		<Add mover="remove_metal_bonds" />
		<Add mover="clear_csts" />
		<Add mover="introduce_mutation" />
		<Add mover="setup_metals" />
		<Add mover="frlx1" />
        </PROTOCOLS>
</ROSETTASCRIPTS>

RemoveMetalConnectionsMover