Release Requirements

This page is a chimera built from:

• User Interface Wishlist
• ChimeraX Presentation Graphics Features Wishlist
• ChimeraX cellPACK Features
• Infrastructure Feature (from developer meeting)

See also Needed Command Functionality and ​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] ​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
  • 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 ​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 ​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 ​Chimera1 movie-related commands)
• Animation GUI (timeline)
• Show multiple frames of a trajectory simultaneously
• Windows app
• Molecular surface mesh, dot styles