subtom_transform_motl

Apply a rotation and a shift to a MOTL file.

This MOTL manipulation script uses one MATLAB compiled scripts below:

subtom_transform_motl

Options

Directories

scratch_dir: Absolute path to the folder with the input to be processed. Other paths are relative to this one.
mcr_cache_dir: Absolute path to MCR directory for the processing.
exec_dir: Directory for executables

Variables

transform_motl_exec: Absolute path to transform_motl executable

File Options

input_motl_fn: Relative path and name of the input MOTL file to be transformed.
output_motl_fn: Relative path and name of the output MOTL file.

Transform Options

shift_x: How much to shift the reference along the X-Axis, applied after the rotations described below.
shift_y: How much to shift the reference along the Y-Axis, applied after the rotations described below.
shift_z: How much to shift the reference along the Z-Axis, applied after the rotations described below.
rotate_phi: Hom much to finally rotate the reference in-plane about it’s final Z-Axis. (i.e. Spin rotation corresponding to phi).
rotate_psi: How much to first rotate the reference about it’s initial Z-Axis. (i.e. Azimuthal rotation corresponding to psi).
rotate_theta: How much to second rotate the reference about it’s intermediate X-Axis. (i.e. Zenithal rotation corresponding to theta).
rand_inplane: If this is set to 1 (i.e. evaluates to true in Matlab) then the inplane rotation of particles will be randomized after the application of the given transform.

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"

transform_motl_exec="${exec_dir}/MOTL/subtom_transform_motl"

input_motl_fn="combinedmotl/allmotl_1.em"

output_motl_fn="combinedmotl/allmotl_transformed_1.em"

shift_x=0.0

shift_y=0.0

shift_z=0.0

rotate_phi=0.0

rotate_psi=0.0

rotate_theta=0.0

rand_inplane=0