New tool: angdist

I just finished putting together a command-line tool to plot a 2D histogram of Euler angles from a set of refined single particles from a cryo-EM dataset (run_* files from RELION). This is a useful visualization to complement the 3D histogram generated by RELION and displayed in relation to the 3D reconstruction. I got the idea from cryoSPARC, which generates and displays the exact same 2D histogram in its 3D refinement jobs (although with a color scale much less friendly to color blind people; I chose to use the “viridis” color scale by default).

The tool can be installed with pip. The code is available here. I also made it citeable with doi:10.5281/zenodo.4104053 .

The starfile library was very helpful. Having this easy way to read STAR files into Python gives me ideas for more tools to produce other useful plots from data found in these files (basically, anything more sophisticated than counting particles in each class, which is so easy to do with AWK that I won’t bother making a Python command-line tool for this).