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,<chain>,<resi1>,<resi2>,<angle>. <chain> is the chain ID, <resi1> is the sequence number of the residue that owns the φ angle, <resi2> is the sequence number of the furthest residue along the chain (in either the N or C direction) containing <resi1> that defines the block of atoms that will undergo rotation, and <angle> 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 <resi1> is in the C direction relative to <resi2>, this is interpreted as a rotation of all atoms N terminal to <resi1> up to <resi2>.

2. PSI: Rotation of a protein subchain about the ψ angle of a particular residue. The syntax for specifying a PSI crotation is PSI,<chain>,<resi1>,<resi2>,<angle>.

3. OMEGA: Rotation of a protein subchain about the ω angle of a particular residue. The syntax for specifying a OMEGA crotation is OMEGA,<chain>,<resi1>,<resi2>,<angle>.

4. CHI1: Rotation of the sidechain χ₁ angle of a particular residue. The syntax for specifying a CHI1 crotation is CHI1,<chain>,<resi>,<angle>. <chain> is the chain ID, <resi> is the sequence number of the residue that owns the χ1 angle, and <angle> 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,<chain>,<resi>,<angle>.

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,<segname_i>,<resi_i>,<atom_i>,<segname_jk>,<resi_j>,<atom_j>,<resi_k>,<atom_k>,<angle>. <segname_i> is the segment ID of the first atom, <resi_i> is the sequence number of the first atom, <atom_i> is the name of the first atom, <segname_jk> is the segment ID of the second and third atoms, <resi_j> is the sequence number of the second atom, <atom_j> is the name of the second atom, <resi_k> is the sequence number of the third atom, <atom_k> is the name of the third atom, and <angle> 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,<chain>,<resi1>,<resi2>,<resi3>. <chain> is the chain ID, <resi1> is the sequence number of the first residue in the helix, <resi2> is the sequence number of the last residue in the helix, and <resi3> is the last residue in the collection of residues whose positions are allowed to move due to the folding. <resi3> can be omitted; if so, only positions of atoms between <resi1> and <resi2> 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,<chain>,<resi_i>,<resi_j>,<atom_i>,<atom_j>,<angle>. <chain> is the chain ID, <resi_i> is the resid (sequence number plus optional insertion code) of the first atom, <resi_j> is the resid of the second atom, <atom_i> is the name of the first atom, <atom_j> is the name of the second atom, and <angle> 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.