UCSF PyEM

UCSF PyEM is a collection of Python modules and command-line utilities for electron microscopy of biological samples.

The entire collection is licensed under the terms of the GNU Public License, version 3 (GPLv3).

Copyright information is listed within each individual file. Current copyright holders include:

• Eugene Palovcak (UCSF)
• Daniel Asarnow (UCSF)

Documentation for the programs can be found in their usage text, comments in code, and in the Wiki of this repository.

Programs

1. projection_subtraction.py - Perform projection subtraction using per-particle FRC normalization.

• recenter.py - Recenter particles on the center-of-mass of corresponding 2D class-averages.
• angdist.py - Graph angular distributions on polar scatter plots. Supports particle subset selection.
• pyem/star.py - Alter .star files. Supports dropping arbitrary fields, Euler angles, etc.
• project.py - Project a map according to .star file entries (angles, CTF, etc.).
• csparc2star.py - Convert Cryosparc metadata files to Relion .star format.

Library modules

1. pyem/mrc.py - Simple, standalone MRC I/O functions.

• pyem/star.py - Parse and write .star files. Uses pandas.DataFrame as a backend.

Other files

1. activate - Place in EMAN2/bin to turn EMAN2 into a Python virtual environment.

(C) 2016 Daniel Asarnow
University of California, San Francisco