Rotate the system around X/Y/Z axes, a specified axis, or via given rotation matrices.

rotate [<mask>] { [x <xdeg>] [y <ydeg>] [z <zdeg>] | axis0 <mask0> axis1 <mask1> <deg> | usedata <set name> [inverse] }

[<mask>] Rotate atoms in <mask> (default all).
[x <xdeg] Degrees to rotate around the X axis.
[y <xdeg] Degrees to rotate around the Y axis.
[z <xdeg] Degrees to rotate around the Z axis.
axis0 <mask0> Mask defining the beginning of a user-defined axis.
axis1 <mask1> Mask defining the end of a user-defined axis.
<deg> Value in degrees to rotate around user defined axis.
usedata <set name> If specified, use 3×3 rotation matrices in specified data set to rotate coordinates.
[inverse] Perform inverse rotation from input rotation matrices.

Rotate specified atoms around the X, Y, and/or Z axes by the specified amounts, around a user-defined axis (specified by <mask0> and <mask1>), or use a previously read in or generated data set of 3×3 matrices to perform rotations. For example, to rotate the entire system 90 degrees around the X axis:

rotate x 90

To rotate residue 270 90 degrees around the axis defined between atoms C1, C2, C3, C4, C5, and C6 in residue 270 and atoms C7, C8, C9, C10, C11, and C12 in residue 270:

rotate :270 axis0 :270@C1,C2,C3,C4,C5,C6 axis1 :270@C7,C8,C9,C10,C11,C12 90.0

To rotate the system with rotation matrices read in from rmatrices.dat:

trajin tz2.norotate.crd
readdata rmatrices.dat name RM mat3x3
rotate usedata RM