Release Requirements

This page is a chimera built from:

• User Interface Wishlist
• Chimera 2 Presentation Graphics Features Wishlist
• Chimera 2 cellPACK Features
• Infrastructure Feature (from developer meeting)

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)
• Molecular surface and volume isosurface styles: solid, mesh

Late summer release

Graphics and tools

• 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

User interface

• Go up and down selection hierarchy
• Save image dialog
• Open file dialog
• Save/restore sessions
• Command history
• Mouse modes
  • button strip
  • hot keys

Infrastructure

• Nightly builds
• Preferences
• Triggers
• Selections
• Session files
  • molecular data
  • Maybe just implement a command history rather than a full session?
• Distinction between public and private API

December release

Presentation graphics

• 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

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 selection

Infrastructure

• Essential commands, make a list with command syntax
• Command documentation
• Full atomspecs

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

Infrastructure

• Reliable operation on Linux
• Application icon
• API documentation

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*)

User interface

• Stereo and orthographic camera modes
• RFE / bug report dialogs
• Chimera 1 -> 2 session conversion

Eventually

Unsorted

• Morphing, trajectory playback*
• Animation commands (frame-argument)
• Animation GUI (timeline)
• Show multiple frames of a trajectory simultaneously
• Windows app