subtom_rotx_motl
Transforms a given MOTL file so that it matches a tomogram rotated or not rotated by IMOD’s ‘clip rotx’ command.
This MOTL manipulation script uses one MATLAB compiled scripts below:
Options
Directories
- tomogram_dir
Absolute path to the folder where the tomograms used in the INPUT motive list are stored.
- 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
- rotx_motl_exec
Rotx motive list 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.
Rotx Options
- tomo_row
Row number of allmotl for tomogram numbers.
- do_rotx
If the following is set to 1 the input MOTL will be transformed in the same way as done by ‘clip rotx’. If it is set to 0 the input MOTL will be transformed by the inverse operation (a positive 90 degree rotation about the X-axis).
Example
tomogram_dir="/net/dstore2/teraraid/dmorado/subTOM_tutorial/data/tomos/bin4"
scratch_dir="${PWD}"
mcr_cache_dir="${scratch_dir}/mcr"
exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"
rotx_motl_exec="${exec_dir}/MOTL/subtom_rotx_motl"
input_motl_fn="../bin4/combinedmotl/allmotl_1.em"
output_motl_fn="combinedmotl/allmotl_1.em"
tomo_row="7"
do_rotx="0"