Software
Phenix
model refinement and validation
Coot
manual model building
ChimeraX
Structure analysis and fancy figures
Chimera
Some people just never forgot the older version
PyMOL
Structure analysis (ask Jerry for license)
cryoSPARC
EM data processing
RELION
EM data processing
EMAN2
EM toolkit
SPIDER
legacy but useful
ColabFold
Where to run AlphaFold
Foldseek
Find your protein fold
DALI server
all-to-all structure alignment