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:
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