subtom_seed_positions

Takes the motive lists made from clicker files in UCSF Chimera and places a number of points at a given spacing along spherical or tubular surfaces.

This MOTL manipulation script uses one MATLAB compiled scripts below:

• subtom_seed_positions

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

seed_pos_exec

Seed positions on motive list executable.

File Options

input_motl_fn_prefix

Relative path and prefix of the input MOTL files to be seeded. The files are expected to have the format input_motl_fn_prefix_#.em where # is the number corresponding to the tomogram corresponding to the motive list and this value will go into row 7 of the output motive list.

output_motl_fn

Relative path and name of the output MOTL file.

Seed Options

spacing

The spacing in pixels at which positions will be added to the surface.

do_tubule

If this is set to 1 (i.e. evaluates to true in Matlab) then the clicker motive list is assumed to correspond to tubules and points will be added along the tubule-axis. Otherwise the clicker file is assumed to correspond to spheres.

rand_inplane

If this is set to 1 (i.e. evaluates to true in Matlab) then the inplane rotation of particles along a tubule will be randomized as opposed to the default which is to place the X-axis orthogonal to the longest tubule axis.

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

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

seed_pos_exec="${exec_dir}/MOTL/subtom_seed_positions"

input_motl_fn_prefix="../startset/clicker"

output_motl_fn="combinedmotl/allmotl_1.em"

spacing=8

do_tubule=0

rand_inplane=0