What a New Team Member Could Work On

These ideas are not listed in any particular order. Maybe we should have a priority ordering. What a new person would do will depend on their interests and skills.

This list should be things the current team members are willing to give to someone else, and are independent enough that they don't require years of built up understanding of how ChimeraX works.

1. Hubmap visualization
   • try to color 3D light microscopy by cell types
2. Medical imaging capabilities (DICOM)
   • visualize segmentation, e.g. tumors
   • try running machine learning segmentation methods.
   • comparing CT or MRI scans over time.
3. Electron microscopy segmentation
   • try current machine learning methods, try to visualize
   • look at what in SimpleITK could be used
4. cryoDRGN visualization
   • run single particle reconstruction on example data and visualize
   • compute specific conformations using neural net
   • use UMAP to visualize conformation space
5. Make how-to videos
   • focus on cool or unusual ChimeraX capabilities
   • export 3D models and embed in web browser with 3D viewer
   • need to have biology background to know what is interesting
   • find exciting new papers and biology systems to show in videos
6. Phenix interaction
   • fragment extension for model building
   • ligand placement in density
7. Many infrastructure projects
   • Python 3.9
   • Qt 6
   • OpenMM packaging (make PyPi package?)
   • Mac arm64 port
   • Vulkan
   • PyPi ChimeraX package (CZI grant)
8. Animation timeline gui
   • scenes are difficult
9. Web services
   • rewrite BLAST gui for better usability (not html) under direction of Elaine
10. APBS electrostatics calculation
    • Add tool to run APBS and PDB2PQR locally and visualize.
    • Then add web service
    • Might develop a way to install optional stuff on the fly to minimize ChimeraX distribution size - ask user if they want to install APBS on first use.
11. Molecular dynamics
    • add minimization with OpenMM
    • try to handle unusual residues as well as possible
    • allow local simulations, a few residues plus mobile shell, plus fixed shell.
    • see if ISOLDE underlying OpenMM layer can be moved into ChimeraX for all tools to use.