ot-tools

A collection of scripts for analysis of cellular cryo-ET data.

Each script has its own set of dependencies, which are listed in the script headers. The python scripts can be run from the shell and can be placed in your $PATH. Most of the scripts in this collection start with "ot_".

Examples of how these scripts are used can be found here: https://www.anaphase.org/papers Thanks to the students who have written or tested these scripts.

nearestneighbour.m

Calculates nearest-neighbor distances in Matlab, from a set of 3-D particle centers.
First use: https://www.ncbi.nlm.nih.gov/pubmed/29742050

ot_nnd.py

Get Nth nearest-neighbor distances from a set of 3-D coordinates. Can substitute for nearestneighbor.m.
First use: https://www.biorxiv.org/content/10.1101/######

ot_rand3Dcoord_rect.py

Generates a random distribution of points with a minimum inter-particle distance in a rectangular box.
First use: https://www.ncbi.nlm.nih.gov/pubmed/29742050

ot_relion_project.py

Average the central N slices in a large number of tomos.
First use: https://www.ncbi.nlm.nih.gov/pubmed/30297429

ot_remap.py

Creates a remapped model from a RELION subtomogram average. The algorithm is inefficient, so run on a machine with lots of cores and a fast SSD.
First use: https://www.ncbi.nlm.nih.gov/pubmed/29742050

ot_rot-ps.py

Rotational power spectrum analysis of a 2-D image.
First use: https://www.ncbi.nlm.nih.gov/pubmed/30504246

ot_unskew.py

Compensate .mod coordinates for compression artifacts.
First use: https://www.ncbi.nlm.nih.gov/pubmed/30297429