ChimeraX possible features for future releases

July 10, 2023 ideas:

• New features we want in ChimeraX
  • Profile grids
  • Machine learning segmentation
  • UMAP
  • Glycan depictions
  • Improved volume rendering effects, medical imaging, tomography
  • Task manager for long running calculations. Allow canceling.
  • Combining sessions
  • GUI for fetching from databases
  • Improved altloc explorer, show multiple altlocs at once
  • Reengineer atomspec parser, crashes on long atom specs, slow
  • Update SteamVR to OpenXR
  • Revise mouse mode support to use manager/provide paradigm and allow in Home tab customization #3928
  • Protein interface analysis

Got through Chimera Tools / Surface binding analysis menu triaging tools to port.

• Chimera features not yet in ChimeraX
  • Scenes
  • Animation
  • MD GUI / ensemble analysis
  • Minimization
  • ViewDockX needs rewrite -- uses html GUI currently
  • Anisotropic ellipsoids
  • Metal coordination analysis
  • Compute sequence alignment from structure superposition
  • Finish render by attribute, selection, worm depiction
  • Ribbon inside color
  • 2D label GUI
  • Lighting GUI
  • Attribute calculator
  • Morph conformations GUI
  • RR Distance Maps
  • Align Chain Sequences
  • Coulombic surface coloring GUI
  • APBS calculation (local or web service)
  • Surface cap GUI
  • Write DMS
  • Morph Map
  • Volume Series

• Chimera features that will not be ported to ChimeraX (unless someone begs)
  • AutoDock Vina
  • MultiDomain Assembler
  • Ribbon style editor
  • MinRMS
  • Ensemble Match
  • Intersurf
  • Surfnet
  • DelPhiController
  • PDB2PQR
  • Constrained move
  • Movement mouse mode (have similar toolbar mouse modes)
  • Add Ions
  • Solvate
  • Write Prmtop (needs old AmberTools)
  • Molecular Dynamics Simulation (mmtk not in python 3)
  • Tile structures GUI (have command)
  • Multiscale Models
  • Small-angle X-ray profile
  • Icosahedron surface
  • Flatten icosahedron
  • Value at atom positions (command exists measure mapvalues)
  • Demo tool, superceded by command-link tutorials
  • Center of rotation GUI
  • Euler angle transforms gui ("Transform Coordinates")
  • Note pad (free text notes to save in session)
  • Movie recorder GUI (freehand recording gives bad movies)
  • Structure diagram (GUI shows 2D image of small molecules)
  • Browser configuration (setup web browser links to open in ChimeraX)
  • Benchmark
  • Palette editor (have a command already)

​Enhancement tickets

Bold items have priority, others are possibilities or wish-list features.

Core user interface

• Fix atom spec parser to handle long lines and run faster (#4842)
• Selection Inspector, mostly done, needs surfaces, volumes
• aliases in menu
• Mouse mode sub-options set by command or gui
• Toolbar customization, add ability for mousemodes to be placed in Home toolbar.
• Mouse mode registration using Manager Provider API.
• Jupyter notebook

Depiction

• saving and restoring scenes (R01)
• animation GUI (R01)
• render by attribute GUI - partly done, needs palette menu, color key button, reverse colors, select by attribute, save defattr file... (NIAID)
• “worms” to show residue attributes, command and gui
• 2D Label GUI (NIAID)
• Surface clip cap GUI - subdivision, color, clip offset, disable
• clipping visual feedback (green disk in chimera)
• per-model clipping gui
• cartoon idealized strands (arcs? planks?) (low priority)
• cartoon inside color
• thermal ellipsoids (low priority)
• show double bonds and triple bonds
• aromatic ring indicator

Structure Analysis

• structure building, almost done, one or two missing tabs, adjust torsions or bond angles (NIAID)
• copy/combine structure models GUI (NIAID)
• Ramachandran plot independent of ISOLDE, have Tristan do it?
• Pocket, tunnels, voids, measurements, CASTP GUI (recipe exists), fetch
• solvate
• add ions
• minimization
• Simple, localized, short molecular dynamics computation
• trajectory analysis other than simple playback, plotting, rmsd calc, clustering, hold steady, per-frame scripts ...
• ensemble clustering
• contact map or fancier RR distance map
• attribute calculator (low priority)
• mcopy (copy settings of a structure to another model) (low priority)
• write selection to text file, info command option
• dssr (RNA structure analysis)

Structure Prediction

• Provide ability to run AlphaFold on paid cloud service such as AWS (R01)
• Deep sequence alignment viewer for alignments found by AlphaFold. (R01)
• Template structure browser -- load and align template PDB structures, show which predicted residues are covered by each PDB.
• AlphaFold distance distogram and observable residue visualization.
• FoldSeek: Fast structure shape searching for PDB and AlphaFold databases

Sequence Analysis

• MAV improvements (R01)
• region browser
• structure matching based on sequence alignment
• fetch UniProt or other annotations onto a sequence alignment
• calculating a multiple sequence alignment from a multiple structure superposition, MatchAlign (#7359)

Volumes

• Phenix user interfaces (Phenix R24)
• Add volume data GUI interfaces (#4306)
• Map subregion selection GUI
• Morph Map GUI
• Volume Filter GUI - Gaussian, Median, Bin, Laplacian, Fourier, Scale, Flatten
• Volume Series GUI
• Map values at atom positions GUI
• Icosahedron Surface GUI

Web Services

• Poisson-Boltzmann electrostatic potential computation GUI [e.g. APBS, probably req: PDB2PQR]

Developer and Chimera user support

• PyPi ChimeraX library (#1470) (CZI)
• Chimera to ChimeraX session converter, volume data support (CZI)
  • Axes/Planes/Centroids
  • Nucleotides
  • ViewDock
  • Sequences
    • "intrinsic"-ness
    • header settings

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.