subtom_scale_noisemotl
Scales a the individual noise motive lists corresponding to a given MOTL file by a given factor. It first concatenates all the necessary input noise motive lists, then scales the motive list by factor and then finally splits the motive list again by tomogram.
This MOTL manipulation script uses three 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
- cat_motls_exec
Concatenate motive lists executable
- scale_motl_exec
Scale motive list executable
- split_motl_by_row_exec
Split MOTL by row executable.
- motl_dump_exec
MOTL dump executable
File Options
- iteration
The iteration of the all particle motive list to process from: input will be all_motl_fn_prefix_iteration.em (define as integer e.g. iteration=1)
- all_motl_fn_prefix
Relative path and prefix to allmotl file from scratch directory.
- input_noise_motl_fn_prefix
Relative path and prefix to input noisemotls.
- output_noise_motl_fn_prefix
Relative path and prefix to output noisemotls.
Tomogram Options
- tomo_row
Row number of allmotl for tomogram numbers.
Scaling Options
- scale_factor
How much to scale up the tomogram coordinate extraction positions (rows 8 through 10 in the MOTL), e.g. To scale from bin8 to bin4 the factor would be 2.
Example
scratch_dir="${PWD}"
mcr_cache_dir="${scratch_dir}/mcr"
exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"
cat_motls_exec="${exec_dir}/MOTL/subtom_cat_motls"
scale_motl_exec="${exec_dir}/MOTL/subtom_scale_motl"
split_motl_by_row_exec="${exec_dir}/MOTL/subtom_split_motl_by_row"
motl_dump_exec="${exec_dir}/MOTL/motl_dump"
iteration="1"
all_motl_fn_prefix="combinedmotl/allmotl"
input_noise_motl_fn_prefix="../bin8/combinedmotl/noisemotl"
output_noise_motl_fn_prefix="combinedmotl/noisemotl"
tomo_row="7"
scale_factor="2"