From aa704d6a70e0711951ebfa01969d3d36c61ecccb Mon Sep 17 00:00:00 2001 From: "Vikram K. Mulligan" Date: Wed, 26 May 2021 18:18:33 -0400 Subject: [PATCH] Add docs for new options. --- .../generalized_kic/GeneralizedKICperturber.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/scripting_documentation/RosettaScripts/composite_protocols/generalized_kic/GeneralizedKICperturber.md b/scripting_documentation/RosettaScripts/composite_protocols/generalized_kic/GeneralizedKICperturber.md index f61770962..20bcdc955 100644 --- a/scripting_documentation/RosettaScripts/composite_protocols/generalized_kic/GeneralizedKICperturber.md +++ b/scripting_documentation/RosettaScripts/composite_protocols/generalized_kic/GeneralizedKICperturber.md @@ -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"**)
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"**)
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"**)
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"**)
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"**)
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