Python programs for electron microscopy
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pyem Call stack for parallel pdistdq. Feb 14, 2019
.gitignore Added ipynb, eman2 logs to .gitignore Dec 17, 2017
LICENSE Licensing, documentation and enhanced feature completeness. Aug 5, 2016
README.md Updated README.md for csparc2star.py. Dec 12, 2016
activate activate script for EMAN2 virtualenv Aug 30, 2016
angdist.py angdist.py Aug 30, 2016
changelog.md rudimentary changelog Sep 17, 2018
csparc2star.py csparc2star.py output merge key Sep 22, 2018
map.py Added final mask argument in map.py Dec 25, 2018
mask.py Refactor --base-map and --overlap to work as expected Aug 23, 2018
par2star.py par2star.py option for cisTEM Relion imports Oct 16, 2018
pose.py Most of pose.py (no plots, untested). Dec 5, 2018
project.py project.py phase flipping support Sep 8, 2018
projection_subtraction.py Move util.convert and util.quat to new geom package. Nov 20, 2018
recenter.py Code cleanup inspections (minor). Feb 13, 2019
reconstruct.py Let relion compute apix if none provided Sep 30, 2017
requirements.txt healpy is required Feb 3, 2019
setup.py added healpy to setup.py Feb 3, 2019
sort.py Added sort.py for projection matching/sorting May 13, 2018
stack.py stack.py Sep 18, 2018
star.py Fix for single merge-field. Feb 13, 2019
star2bild.py star2bild.py added --class Jul 23, 2018
subparticles.py Code cleanup inspections (minor). Feb 13, 2019
subset.py subset.py maintenance. Dec 5, 2018
varmap.py Corrected varmap.py. Dec 5, 2018

README.md

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