/dynamo2relion

Converts Dynamo tables to star files for coordinate import into RELION 4.0

Primary LanguagePythonBSD 3-Clause "New" or "Revised" LicenseBSD-3-Clause

Dynamo2Relion

A Tiny Function to Convert Dynamo Tables to Star Files for RELION 4.0

PyPI pyversions

Based on dynamo2m by Alister Burt.

Installation

Installation is carried out via:

pip install dynamo2relion

Requirements

Your directory containing the tilt series directories must be structured as follows:

tilt_series_directory #Directory containing all TS directories, link to this directory
|
--> TS_01 #Directory containing TS_01              
       |
       --> TS_01.mrc #TS_01  image stack. The file extension does not matter.        
|
--> TS_02              
       |
       -->TS_02.mrc  #
|
--> etc...

The program will ask you the path to tilt_series_directory. No directories other than the TS_* directories should be present in tilt_series_directory. Naming convention for the TS_* directories can be any mix of upper of lower case TS and any numbering convention desired.

Usage

Instructions for use can be found via typing:

dynamo2relion --help

For binning level, simply enter 1 if the coordinates of your particles in the Dynamo table were picked from an unbinned tomogram. If the tomograms the particles were picked in were binned, add the correct binning level: binning is done using IMOD convention, i.e. for a pixel size of 1 A/px, a binning level of 8 would yield 8 A/px.