= Release Requirements =

This page is a chimera built from:
 - [wiki:EarlyUI User Interface Wishlist]
 - [wiki:PresentationGraphics ChimeraX Presentation Graphics Features Wishlist]
 - [wiki:CellPack ChimeraX cellPACK Features]
 - [wiki:2015-4-2 Infrastructure Feature (from developer meeting)]

See also [[Needed Command Functionality]] and [http://www.cgl.ucsf.edu/home/meng/chi2/command-structure.html Command-Structure Thoughts]

== Mostly done.  May need cleaning up. ==

=== Graphics and tools ===
 - ~~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)
 - ~~Set of built-in colors (as opposed to giving hex code or RGBs only)
 - ~~Fixed mouse modes
 - ~~Standard open file dialog


== Late summer release ==

 === Graphics and tools ===
 - ~~Ribbons [Elaine] [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html Ribbons and Other Image Issues, Pymol comparisons]
   - ~~hides mainchain atoms, sidechain connects to ribbon nicely
   - ~~Natural cubic spline with parallel transport frame twists [ Conrad]
   - Smooth secondary structure ribbons [Conrad]
   - Subdivision quality
 - ~~Molecular surface
   - ~~[wiki:SurfaceCategories molecular surface categories*] [TomG surface command suggestions, Elaine category thoughts] 
   - ~~is a surface a separate model?  (specification, transformation, etc) [Conrad]
     - ~~Surface model shares the same model number as molecular but different sub-model number
   - ~~easily hide smaller bits (like "surf visiblePatches N")
 - ~~Atom, bond subdivision control [TomG]
 - ~~Balloon atomspec (mouse-over status message) [TomG]
 - ~~Intra-molecular pseudobonds (metal complexation, missing segments) [TomG and Greg]
   - ~~Display style (thin sticks?, dashed cylinders?, dashed lines?)

 === User interface ===
 - ~~Go up and down selection hierarchy [TomG]
  - go above models, e.g., NMR ensembles
 - ~~Save image dialog on File menu [Conrad]
 - Save/restore sessions [Conrad, Eric, TomG, Greg]
 - ~~Command history [Eric]
   - ~~Save commands dialog [Eric]
 - ~~Mouse selection [TomG]
   - ~~Atom selection [TomG]
   - ~~Bond and pseudobond selection [TomG]
   - ~~Ribbon selection [Conrad]
   - ~~decide whether click or ctrl-click selects
 - ~~Help system
  - ~~add command help links in log

 === Infrastructure ===
 - ~~Nightly builds [Conrad]
   - ~~Mac [Conrad]
   - ~~Linux [Greg]
 - ~~CLI API for command history [Greg]
 - ~~Preferences and caches [Greg]
   - ~~Settings [Eric]
 - ~~Threading model [All]
 - Triggers (Python) [Greg,Conrad]
   - What are the "standard" UI triggers?
   - ~~"Check for changes" trigger (when and how)?
 - Notifications (C++) and link to triggers
   - ~~What are the associated triggers and when are they invoked? [Eric,Greg]
   - ~~Implement [https://plato.cgl.ucsf.edu/trac/chimerax/wiki/Notifications proposal] [Eric]
 - Unify atomspec and mouse click selections [TomG]
 - ~~Mouse mode registration [TomG]
 - Session files
   - molecular data (blob I/O [Eric,Greg], open state like transformations)
   - camera, lighting, background color, etc. [Greg]
   - metadata, thumbnail in particular or use OS file metadata [TomG]
 - Distinction between public and private API [All]


== December release ==

 === Presentation graphics ===
 - ~~Transparency controllable down to individual atoms/bonds, small units of other reps
   - ~~single-layer
 - ~~Clipping
   - ~~global hither/yon
   - ~~capping of surfaces
   - ~~single-plane or slab, moves with models
 - ~~Selection highlight
 - ~~Inter-molecular pseudobonds (distances, hydrogen bonds)

 === CellPACK ===
 - Open cellPACK models, fetching JSON files from web
 - Open collada surface files used to represent cellPACK molecules
 - Hierarchical collapsible list of model components
  - checkbuttons for display, active, etc.
 - Mouse hover to pop-up name of molecular component

 === User interface ===
 - Simple !Selection/Action menus
  - Actions
   - Hide/show
   - Color
   - Surface
   - Style (atom only)
   - Delete
  - Selections
   - By model/chain
   - By structure (ions, ligand, secondary structure, etc.)
   - Operations (clear, invert all models, invert selected models, select all)
 - Rapid Access (file history in particular)
 - Hierarchical model panel
  - Active/shown checkboxes
  - Action buttons
 - Full side view (clipping planes)
 - ~~Mouse modes [TomG]
  - ~~button strip
  - ~~modifier keys?
 - ~~Fixed center of rotation for focus command. [TomG]
 - Replayable? record of executed commands (both cli and menu)
 - Help
  - tool help: ~~access through context menu

 === Infrastructure ===
 - Essential commands, make a list with command syntax
    - Elaine [[Needed Command Functionality]]
    - Elaine [http://www.cgl.ucsf.edu/home/meng/chi2/command-structure.html Command-Structure Thoughts]
 - Command documentation
 - Full atomspecs
 - Model hierarchy, display state inherits? how to show child without parent

== Highly desirable ==

 === Graphics and tools ===
 - Smart molecule display
 - Transparency correctly rendered multiple-layer, multiple models
 - 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)
 - Isosurface smoothing
 - Easily hide smaller surface components (like hide dust)
 - Geometric objects 
  - structure-derived (best-fit planes, axes, ellipsoids, etc.)*
  - arbitrary (3D arrows, planes to cast shadows upon, etc.)
 - Scenes (so that one doesn't have to have a session for each figure panel)
 - Background color gradient
 - Other sectioning (e.g. cut octant, spherical clipping, etc.)
 - 3D labels
 - 2D labels and arrows of adjustable color/size, interactive repositioning
 - Color key (specialized 2D annotation)

 === CellPACK ===
 - Geometric selection eg drag-select and select-within-shape

 === User interface ===
 - Actions
  - Style
   - ribbon
   - surface
  - Label
 - Selections
  - By residue type or category/atom element
  - By chemistry (functional groups, atom types, residue properties)
 - Appearance (transparency and material)
 - Export in different formats (PDB, volume format, graphics format, etc)
 - Improved toolshed interface
 - Remember graphics window / tools layout in sessions
 - Tool bar

 === Infrastructure ===
 - Reliable operation on Linux
 - ~~Application icon
 - API documentation
 - Separate fetching from I/O format registration
 - Tool icon access

== Would be nice ==

 === Graphics and tools ===
 - Ribbons fully integrated with pipes and planks 
  - (alternative ways of "cartooning" the secondary structure elements)
 - Tubes (could be a sub-option of ribbons)
 - 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?
  - Individual surface triangles?
 - 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
 - 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)
 - Interactively adjustable light positions
 - Lighting contrast slider
 - Background images
 - Publication presets?  hard to decide because there are so many potentially useful combinations of styles and lighting
 - Clashes*
  - (find contacts also important for coloring interaction patches of surfaces*)
 - Clip capping of ribbons, atoms/bonds
 - Per-model clipping

 === User interface ===
 - Stereo and orthographic camera modes
 - RFE / bug report dialogs
 - Chimera 1 -> 2 session conversion
 - Custom ("Miller browser") open dialog with embeddable frame?
 - Save graphics window / tools layouts; offer "preset" layouts
 - Mouse modes hot keys?

 === Infrastructure ===
 - Tool import API for possibly uninstalled tool

== Eventually ==

 === Unsorted ===
 - Morphing, trajectory playback*
 - Animation commands (frame-argument) (see [http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands Chimera1 movie-related commands])
 - Animation GUI (timeline)
 - Show multiple frames of a trajectory simultaneously
 - Windows app
 - Molecular surface mesh, dot styles