Presentation Graphics Features Wishlist

asterisk = requires some analysis code

Required

• For late summer
  • sessions (required because one needs to save state for any pub figure)
  • ribbons
    • hides mainchain atoms, sidechain connects to ribbon nicely
  • molecular surface
    • molecular surface categories* (I think the default should have a separate "main" for each chain ID)
    • easily hide smaller bits (like "surf visiblePatches N")
  • smoothness control (vertex density, subdivision)
  • balloon atomspec
  • pseudobonds
    • metal complexation
    • distance monitor
• For December
  • transparency controllable down to individual atoms/bonds, small units of other reps
    • single-layer
  • clipping
    • global hither/yon
    • capping of all solids: surfaces, ribbons, atoms/bonds, objects
    • per-model single-plane or slab
  • selection highlight

• Partially done? More clean up.
  • atom/bond styles: sticks, bs, sphere, individually controllable
  • show/hide controllable down to individual atoms, small units of other reps
  • coloring controllable down to individual atoms, small units of other reps
  • silhouettes
  • adjustable background color
  • interactive shadows
  • lighting options - ambient occlusion, ambient-only, N-point
  • supersampling
  • volume isosurfaces
  • depth cueing (want adjustable color, amount)

Highly desirable

• Smart molecule display
• 3D labels
• transparency correctly rendered multiple-layer, multiple models
• isosurface smoothing
• scenes (so that one doesn't have to have a session for each figure panel)
• easily hide smaller surface components (like hide dust)
• background color gradient
• other sectioning (e.g. cut octant, spherical clipping, etc.)
• 2D labels and arrows of adjustable color/size, interactive repositioning
• color key (specialized 2D annotation)
• geometric objects
  • structure-derived (best-fit planes, axes, ellipsoids, etc.)*
  • arbitrary (3D arrows, planes to cast shadows upon, etc.)
• color by atom/res attribute (e.g. hydrophobicity)*, geometry (e.g. radial), or volume data value (e.g. density, electrostatic potential)*
• H-bonds*
• dashed and dotted pseudobonds (cylinders as well as lines)

• Done?
  • set of built-in colors (as opposed to giving hex code or RGBs only)
  • molecular surface and volume isosurface styles: solid, mesh

Would be nice

• clashes*
  • (find contacts also important for coloring interaction patches of surfaces*)
• interactively adjustable light positions
• lighting contrast slider
• background images
• ribbons fully integrated with pipes and planks
  • (alternative ways of "cartooning" the secondary structure elements)
• tubes (could be a sub-option of ribbons)
• abstracted nucleotides - slabs, lollipops, ladder rungs
  • (need better default than in Chimera1)
• per-model silhouette
• custom silhouette
  • draw outline in 2D with mouse, regular geometric (e.g. circular) and maybe even free-form with smoothing?
  • other ways to emphasize area of interest within an outline
    • making stuff outside it transparent, faded, or blurred
• individual surface triangles?
• continuous fade between residue ribbon segments instead of abrupt
• ring fill, aromaticity and bond multiplicity displays
  • (e.g. two lines or two sticks for double bonds)
• option to show solvent-accessible vs. solvent-excluded, or both
• ways to control and smooth boundary of displayed patch, maybe drawing an outline with mouse or choosing individual triangles to hide?
• some kind of shininess control and/or ability to use different material properties for different objects
• "smart" clipping (keeping objects whole, e.g. multiscale subunits not sliced even if plane goes through them)
• publication presets? hard to decide because there are so many potentially useful combinations of styles and lighting

Eventually

• morphing, trajectory playback*
• animation commands (frame-argument)
• animation GUI (timeline)
• show multiple frames of a trajectory simultaneously