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

References:

• Asarnow, D., Palovcak, E., Cheng, Y. UCSF pyem v0.5. (Zenodo:2019)

• Example usage of Pyem on Biowulf:
  Protocol on Transforming Cryosparc .cs file to RELION .star file for Bayesian Polishing (PDF)

• UCSF Pyem Github page:
  https://github.com/asarnow/pyem

• Note the version differences on csparc2star.py:
  Load version after pyem/230821 on Biowulf to run csparc2star.py, result from older version will contain unwanted ">" charater in the generated .star file.
• Note the version differences on star.py:
  Load version before pyem/230315 to copy Micrograph path and particle coordinates via star.py, otherwise unwanted columnes will be added to the generated .star file.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load pyem
[user@cn3144 ~]$ csparc2star.py  J76_particles_exported.cs  csparc_P6_J76_particles_exported.star

Copy Micrograph path and particle coordinate from original particle .star file: see detailed protocol

[user@cn3144 ~]$star.py --copy-micrograph-coordinates JoinStar/job053/join_particles.star  \
> csparc_P6_J76_particles_exported.star  csparc_P6_J76_particles_exported_Micrograph_Added.star
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$