= 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