.. _subs_buildtasks_psfgen_mods_crotations: crotations ---------- A ``crotations`` directive is used to specify rotations about rotatable dihedral bonds to reposition parts of the protein. There are 8 types of ``crotations`` 1. ``PHI``: Rotation of a protein subchain about the φ angle of a particular residue. The syntax for specifying a ``PHI`` crotation is ``PHI,,,,``. ```` is the chain ID, ```` is the sequence number of the residue that owns the φ angle, ```` is the sequence number of the furthest residue along the chain (in either the N or C direction) containing ```` that defines the block of atoms that will undergo rotation, and ```` is the angle of rotation in degrees. For example, ``PHI,A,12,15,180`` would rotate residues 12 through 15 in chain A by 180 degrees about the φ angle of residue 12. If ```` is in the C direction relative to ````, this is interpreted as a rotation of all atoms N terminal to ```` up to ````. 2. ``PSI``: Rotation of a protein subchain about the ψ angle of a particular residue. The syntax for specifying a ``PSI`` crotation is ``PSI,,,,``. 3. ``OMEGA``: Rotation of a protein subchain about the ω angle of a particular residue. The syntax for specifying a ``OMEGA`` crotation is ``OMEGA,,,,``. 4. ``CHI1``: Rotation of the sidechain χ₁ angle of a particular residue. The syntax for specifying a ``CHI1`` crotation is ``CHI1,,,``. ```` is the chain ID, ```` is the sequence number of the residue that owns the χ1 angle, and ```` is the angle of rotation in degrees. For example, ``CHI1,A,12,180`` would rotate the χ₁ angle of residue 12 in chain A by 180 degrees. 5. ``CHI2``: Rotation of the sidechain χ₂ angle of a particular residue. The syntax for specifying a ``CHI2`` crotation is ``CHI2,,,``. 6. ``ANGLEIJK``: Rotation of an entire protein segment around the axis defined by the cross product normal to the angle made by three identied atoms; the atom identified as ``i`` can be in its own segment, but ``j`` and ``k`` must be in the same segment (all three can be in the same segment as well). The two vectors considered are those that point from atom ``i`` to atom ``j`` and from atom ``j`` to atom ``k``. All atoms in atom ``j``'s and ``k``'s segment will rotate about the cross product of these two vectors. The syntax for specifying an ``ANGLEIJK`` crotation is ``ANGLEIJK,,,,,,,,,``. ```` is the segment ID of the first atom, ```` is the sequence number of the first atom, ```` is the name of the first atom, ```` is the segment ID of the second and third atoms, ```` is the sequence number of the second atom, ```` is the name of the second atom, ```` is the sequence number of the third atom, ```` is the name of the third atom, and ```` is the angle of rotation in degrees. For example, ``ANGLEIJK,A,12,N,B,15,C,18,O,180`` would rotate all atoms in segment B by 180 degrees about the angle defined by atoms N (in residue 12 of segment A), C (in residue 15 of segment B), and O (in residue 18 of segment B). 7. ``ALPHA``: Fold specified subchain into an α helix. The syntax for specifying an ``ALPHA`` crotation is ``ALPHA,,,,``. ```` is the chain ID, ```` is the sequence number of the first residue in the helix, ```` is the sequence number of the last residue in the helix, and ```` is the last residue in the collection of residues whose positions are allowed to move due to the folding. ```` can be omitted; if so, only positions of atoms between ```` and ```` inclusive are repositioned. For example, ``ALPHA,A,12,15,18`` would fold residues 12 through 15 in chain A into an α helix, and atoms up to and including residue 18 are repositioned as a result. 8. ``GLYCAN_PENDANT``: Rotation of a glycan pendant about the bond between two specified atoms. The syntax for specifying a ``GLYCAN_PENDANT`` crotation is ``GLYCAN_PENDANT,,,,,,``. ```` is the chain ID, ```` is the resid (sequence number plus optional insertion code) of the first atom, ```` is the resid of the second atom, ```` is the name of the first atom, ```` is the name of the second atom, and ```` is the angle of rotation in degrees. For example, ``GLYCAN_PENDANT,A,12,15,C1,O4,90`` would rotate the glycan pendant connected between atoms C1 (in residue 12 of chain A) and O4 (in residue 15 of chain A) by 90 degrees. Atoms i and j must be bonded by a rotatable bond, otherwise no rotation will occur. The bond between i and j must define a pendant group; that is, atom j and all atoms connected to it (except for atom i) will be rotated about the bond between i and j.