subtom_scale_motl

Scales a given MOTL file by a given factor. It also resets the shifts in the motive list (rows 11 to 13) to values less than 1 so that with a given scale factor of 1, it can apply the shifts to the tomogram coordinates (rows 8 to 10) so that particles can be reextracted better centered to allow for tighter CC masks to be used in further iterations of alignment.

This MOTL manipulation script uses one MATLAB compiled scripts below:

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

scale_motl_exec

Scale motive list executable

File Options

input_motl_fn

Relative path and name of the input MOTL file to be unbinned.

output_motl_fn

Relative path and name of the output MOTL file.

Scaling Options

scale_factor

How much to scale up the tomogram coordinate extraction positions (rows 8 through 10 in the MOTL) and the particle shifts (rows 11 through 13).

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

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

scale_motl_exec="${exec_dir}/MOTL/subtom_scale_motl"

input_motl_fn="../bin8/combinedmotl/allmotl_1.em"

output_motl_fn="combinedmotl/allmotl_1.em"

scale_factor=2