subtom_clean_motl

Cleans a given MOTL file based on distance and/or CC scores.

This MOTL manipulation script uses one MATLAB compiled scripts below:

• subtom_clean_motl

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

clean_motl_exec

Clean MOTLs executable

File Options

input_motl_fn

Relative path and name of the input MOTL file to be cleaned.

output_motl_fn

Relative path and name of the output MOTL file.

output_stats_fn

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

The CSV format of the output statistics file for cleaning is a single row with the following columns:

Column	Value
1	Total Initial Number of Particles
2	Number of Particles Removed in Edge Cleaning
3	Number of Particles Removed in Cluster Cleaning
4	Number of Particles Removed in Distance Cleaning
5	Number of Particles Removed in CC Cleaning
6	Total Remaining Number of Particles

Clean Options

tomo_row

Which row in the motl file contains the correct tomogram number. Usually row 5 and 7 both correspond to the correct value and can be used interchangeably, but there are instances when 5 contains a sequential ordered value starting from 1, while 7 contains the correct corresponding tomogram.

do_ccclean

If the following is set to 1 then the MOTL will be cleaned by CCC either by CCC value or a fraction of the highest CCC values to keep. If it is set to 0 then CCC cleaning will be skipped.

cc_fraction

If cleaning by CC then after edge, cluster, and distance cleaning, if any are selected, is completed. The MOTL will be sorted by CCC and then the top fraction as specified here will be kept with the rest discarded. For example if cc_fraction=0.7 the top 70% of the clean data will be kept and the bottom 30% of the cleaned data will be discarded. A value of 1 here means that data is not cleaned by CCC fraction.

cc_cutoff

If cc_fraction is 1 and therefore not used then particles with a CCC below this cutoff will be removed from the output MOTL file. Values must be within -1 to 1, with -1 not removing any particles.

do_distance

If the following is set to 1 then the MOTL will be cleaned by distance. If it is set to 0 distance cleaning will be skipped.

distance_cutoff

Particles that are less than this distance in pixels from another particle will be cleaned with the particle with the highest CCC kept while the others are removed from the output MOTL file.

do_cluster

If the following is set to 1 then the MOTL will be cleaned by a clustering criteria that enforces kept particles to exist as clusters. This can be useful when there is no lattice and clusters of particles makes a good indication that a true copy of the reference exists there. If it is set to 0 cluster cleaning will be skipped.

cluster_distance

The following determines the radius that defines what is considered a cluster in cluster cleaning.

cluster_size

The cluster size specifies how many particles must be found within cluster_distance for the particle to be considered part of a cluster. The particle with the highest CCC in the cluster will be selected as the representative particle for the cluster and the remaining clustered points will be removed.

do_edge

If the following is set to 1 then the MOTL will be edge cleaned considering the dimensions of the tomogram in which the particles are contained. If any part of the particle exists outside of the tomogram it will be removed from the MOTL. If it is set to 0 edge cleaning will be skipped.

tomogram_dir

Absolute path to the folder where the tomograms are stored. If you are not edge cleaning leave this set to “”.

box_size

What is the box size of the particle that will be extracted from the tomogram, which is necessary to specify to be able to edge clean.

write_stats

If the following is 1 then the details of how many particles were cleaned in each stage 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"

clean_motl_exec="${exec_dir}/MOTL/subtom_clean_motl"

input_motl_fn="combinedmotl/allmotl_2.em"

output_motl_fn="combinedmotl/allmotl_cc0.1_dist4_cluster2d10_2.em"

output_stats_fn="combinedmotl/allmotl_cc0.1_dist4_cluster2d10_stats.csv"

tomo_row=7

do_ccclean=1

cc_fraction=1

cc_cutoff=0.1

do_distance=1

distance_cutoff=4

do_cluster=1

cluster_distance=10

cluster_size=2

do_edge=1

tomogram_dir="/net/dstore2/teraraid/dmorado/subTOM_tutorial/data/tomos/bin8"

box_size=36

write_stats=1