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  • Demo tool, superceded by command-link tutorials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