SymmetricCycpepAlignMover

Documentation created by Vikram K. Mulligan (vmullig@uw.edu), Baker laboratory, on 23 December 2016. Back to Mover page.

SymmetricCycpepAlignMover

Table of Contents

Description

Given a quasi-symmetric cyclic peptide, this mover aligns the peptide so that the cyclic symmetry axis lies along the Z-axis and the centre of mass is at the origin. It then optionally removes all but one symmetry repeat, so that true symmetry may be set up with the SetupForSymmetry mover.

Note that, if the trimming option is used, all non-protein residues (e.g. crosslinkers like 1,3,5-tris(bromomethyl)benzene) are also removed. A new fold tree is set up with the middle of the symmetry repeat as the root of the tree (which tends to be useful for subsequent symmetric minimization).

Full options

<SymmetricCycpepAlign name=(string) auto_detect_symmetry=(bool,"false")
    symmetry_repeats=(int,"2") mirror_symmetry=(bool,"false")
    angle_threshold=(real,"10.0") trim_to_single_repeat=(bool,"false")
    repeat_to_preserve=(int,"1") invert=(bool,"false")
/>

name (string) A unique name for this instance of the mover, used to refer to the mover later on in the script.
auto_detect_symmetry (bool) If true, the symmetry of this peptide will be detected automatically. The mover will exit with failure status (halting the trajectory but not terminating program execution) if the peptide is asymmetric. False by default. (Note that if this is set to "true", the "symmetry_repeats" and "mirror_symmetry" options cannot be used.)
symmetry_repeats (int) The number of symmetry repeats. For example, to specify c6 or c6/m symmetry, set this to "6". Defaults to "2" (for c2 symmetry). The mover will terminate with failure status if the symmetry of the input peptide does not match this symmetry.
mirror_symmetry (bool) If true, this indicates that the pose possesses mirror symmetry. For example, to specify c6/m symmetry, set "symmetry_repeats" to "6" and "mirror_symmetry" to "true". If set to "false", this would indicate c6 symmetry. Defaults to "false" (for c2 symmetry with no mirroring).
angle_threshold (real) The cutoff, in degrees, for considering two dihedral values to be equal. Defaults to 10 degrees. This is used when confirming that a quasi-symmetric peptide has the indicated symmetry, or for detecting the symmetry of the peptide.
trim_to_single_repeat (bool) If true, all geometry in the peptide (including all crosslinkers) will be deleted, except for the polypeptide part of a single symmetry repeat. Defaults to "false". (This is useful for setting up a peptide for the SetupForSymmetry mover).
repeat_to_preserve (int) If "trim_to_single_repeat" is true, then this is the symmetry repeat that will NOT be deleted (i.e. the one that will be preserved). Defaults to "1".
invert (bool) If true, the peptide normal is aligned to the negative Z-axis; if false, it is aligned to the positive. Default false.

Example

This script operates on a 20-residue c4-symmetric peptide. A peptide bond connecting the N and C termini is declared with the DeclareBond mover, and the peptide is then aligned to the Z-axis and trimmed to a single 5-residue symmetry repeat with this mover. The SetupForSymmetry mover is then used to set up Rosetta symmetry, and a new bond between the individual symmetry repeats is declared using the PeptideCyclizeMover, which also creates constraints for the peptide bond. Finally, the peptide is subjected to symmetric relaxation.

<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ScoreFunction name="bnv" weights="beta_nov15.wts" symmetric="true" />
		<ScoreFunction name="bnv_cst" weights="beta_nov15_cst.wts" symmetric="true" />
	</SCOREFXNS>
	<RESIDUE_SELECTORS>
		<!-- A selector is needed because the SetupForSymmetry mover appends virtual residues, -->
		<!-- and the PeptideCyclizeMover, by default, operates on the first and last residues  -->
		<!-- of the pose or selection.                                                         -->
		<Index name="peptide_selector" resnums="1-20" />
	</RESIDUE_SELECTORS>
	<MOVERS>
	
		<DeclareBond name="bond1" res1="20" res2="1" atom1="C" atom2="N" add_termini="false" />
	
		<SymmetricCycpepAlign name="align" auto_detect_symmetry="true" angle_threshold="15" trim_to_single_repeat="true" invert="true" />
		
		<SetupForSymmetry name="sym" definition="inputs/c4.symm" />

		<PeptideCyclizeMover name="bond2" residue_selector="peptide_selector" />
		
		<FastRelax name="frlx" repeats="3" scorefxn="bnv_cst" >
			<MoveMap name="frlx_mm1" >
				<Span begin="1" end="999" bb="true" chi="true" />
				<Jump number="1" setting="true" />
				<Jump number="2" setting="true" />
				<Jump number="3" setting="true" />
				<Jump number="4" setting="true" />
				<Jump number="5" setting="true" />
				<Jump number="6" setting="true" />
				<Jump number="7" setting="true" />
				<Jump number="8" setting="true" />
				<Jump number="9" setting="true" />
				<Jump number="10" setting="true" />
				<Jump number="11" setting="true" />
				<Jump number="12" setting="true" />
			</MoveMap>
		</FastRelax>
		
	</MOVERS>
	<PROTOCOLS>
		<Add mover="bond1" />
		<Add mover="align" />
		<Add mover="sym" />
		<Add mover="bond2" />
		<Add mover="frlx" />
	</PROTOCOLS>
	<OUTPUT scorefxn="bnv" />
</ROSETTASCRIPTS>

SymmetricCycpepAlignMover