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"