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Document new perturber options for GeneralizedKIC and dibenzyl ether crosslinker in the CrosslinkerMover #46

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Expand Up @@ -53,6 +53,8 @@ Certain types of perturbers operate on residues, and require a list of one or mo
10. Randomly select mainchain torsions from within a mainchain torsion bin (**effect="set_backbone_bin"**)<br/>This perturber takes a user-specified bin and bin transitions probability file, and randomly chooses mainchain torsions for specified residues from within that bin. The perturber has two additional input options: a [[bin transitions probability file|Bin-transition-probabilities-file]] (**bin_params_file="filename.bin_params"**) and a bin (**bin="binname"**), where the bin must match a bin named in the bin transitions probability file. Note that the selection of torsion angles from within a bin is based on the sub-bin distribution specified in the bin transitions probability file; it can be uniform or based on the Ramachandran distribution for an alpha-amino acid. (See the [[file type documentation|Bin-transition-probabilities-file]] for details on this.)
11. Copy mainchain torsion values from another residue (**effect="copy_backbone_dihedrals"**)<br/>This perturber will copy all mainchain torsion values from one residue in the loop to be closed (in which case, previous perturbers may have altered _that_ residue's dihedral values) or in the rest of the pose to the current loop residue. Subsequent perturbers may then alter this residue's torsions. This is useful for quasi-symmetric sampling. This perturber takes a list of residue indices, where the first residue is the residue from which torsion values will be copied, and the second, third, fourth, _etc._ are the residues to which values will be copied. All residues listed must have the same number of mainchain torsions.
12. Mirror another residue's mainchain torsion values (**effect="mirror_backbone_dihedrals"**)<br/>This is just like the **"copy_backbone_dihedrals"** effect, but mainchain torsion values will be inverted in the process. This is useful for quasi-symmetric sampling with mirror symmetry. Like the **"copy_backbone_dihedrals"** perturber, this one takes a list of residues, where the torsions of the first are mirrored and the inverted values are used to set the torsions of the second, third, fourth, _etc._
13. Copy a particular torsion value from elsewhere (**effect="copy_dihedral"**)<br/>This perturber will copy a single torsion value (mainchain or otherwise) from one position in the loop to be closed. Subsequent perturbers may then alter this torsions. This is useful for quasi-symmetric sampling. This perturber takes a list of lists of atoms defining dihedrals, where the first dihedral is the one from which the torsion value will be copied, and the second, third, fourth, _etc._ are the dihedrals to which the value will be copied.
14. Copy a particular torsion value from elsewhere with mirroring (**effect="mirror_dihedral"**)<br/>This perturber will mirror a single torsion value (mainchain or otherwise) from one position in the loop to be closed. It takes a list of lists of atoms defining dihedrals, where the first dihedral is the one from which the torsion value will be copied, and the second, third, fourth, _etc._ are the dihedrals to which the value will be copied with mirroring.

## Shorthands

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