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