subtom_compare_motls

Compares the translations and rotations between two MOTLS of different iterations of alignment.

This MOTL manipulation script uses one MATLAB compiled scripts below:

• subtom_compare_motls

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

compare_motls_exec

Comparison MOTLs executable

File Options

motl_1_fn

Relative path and name of the first MOTL file

motl_2_fn

Relative path and name of the second MOTL file

output_diffs_fn

Relative path and name of the optional output difference CSV file. If you do not want to write out the differences just leave this as “”.

The CSV format of the output differences file for comparison is one row per particle in the motive list that has six columns, and a special final line with 22 columns for statistics of differences for the whole motive list. The particle columns are as follows:

Column	Value
1	Particle Index (Motive List row 4)
2	CCC Score for particle in first motive list
3	CCC Score for particle in second motive list
4	Coordinate displacement between motive lists
5	Angular displacement between motive lists
6	Angular displacement ignoring inplane rotations

The special final line columns are as follows:

Column	Value
1	Mean Coordinate displacement between MOTLs
2	Median Coordinate displacement between MOTLs
3	Coordinate displacement standard deviation
4	Maximum Coordinate displacement between MOTLs
5	Mean Angular displacement between MOTLs
6	Median Angular displacement between MOTLs
7	Angular displacement standard deviation
8	Maximum Angular displacement between MOTLs
9	Same as 5 but ignoring inplane rotations
10	Same as 6 but ignoring inplane rotations
11	Same as 7 but ignoring inplane rotations
12	Same as 8 but ignoring inplane rotations
13	Mean CCC score in the first motive list
14	Median CCC score in the first motive list
15	CCC standard deviation in first motive list
16	Minimum CCC score in the first motive list
17	Maximum CCC score in the first motive list
18	Mean CCC score in the second motive list
19	Median CCC score in the second motive list
20	CCC standard deviation in second motive list
21	Minimum CCC score in the second motive list
22	Maximum CCC score in the second motive list

Comparison Options

write_diffs

If the following is 1 then the differences will be written out, if 0 then not.

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

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

compare_motls_exec="${exec_dir}/MOTL/subtom_compare_motls"

motl_1_fn="combinedmotl/allmotl_1.em"

motl_2_fn="combinedmotl/allmotl_2.em"

output_diffs_fn="combinedmotl/allmotl_1_2_diffs.csv"

write_diffs=1