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