| | 1 | = Release Requirements = |
| | 2 | |
| | 3 | == Mostly done. May need cleaning up. == |
| | 4 | |
| | 5 | === Graphics and tools === |
| | 6 | - Atom/bond styles: sticks, bs, sphere, individually controllable |
| | 7 | - Show/hide controllable down to individual atoms, small units of other reps |
| | 8 | - Coloring controllable down to individual atoms, small units of other reps |
| | 9 | - Silhouettes |
| | 10 | - Adjustable background color |
| | 11 | - Interactive shadows |
| | 12 | - Lighting options - ambient occlusion, ambient-only, N-point |
| | 13 | - Supersampling |
| | 14 | - Volume isosurfaces |
| | 15 | - Depth cueing (want adjustable color, amount) |
| | 16 | - Set of built-in colors (as opposed to giving hex code or RGBs only) |
| | 17 | - Molecular surface and volume isosurface styles: solid, mesh |
| | 18 | |
| | 19 | |
| | 20 | == Late summer release == |
| | 21 | |
| | 22 | === Graphics and tools === |
| | 23 | - Sessions (required because one needs to save state for any pub figure) |
| | 24 | - Ribbons |
| | 25 | - hides mainchain atoms, sidechain connects to ribbon nicely |
| | 26 | - Molecular surface |
| | 27 | - molecular surface categories* (I think the default should have a separate "main" for each chain ID) |
| | 28 | - easily hide smaller bits (like "surf visiblePatches N") |
| | 29 | - Smoothness control (vertex density, subdivision) |
| | 30 | - Balloon atomspec |
| | 31 | - Pseudobonds |
| | 32 | - metal complexation |
| | 33 | - distance monitor |
| | 34 | |
| | 35 | === User interface === |
| | 36 | - Go up and down selection hierarchy |
| | 37 | - Save image dialog |
| | 38 | - Open file dialog |
| | 39 | - Save/restore sessions |
| | 40 | - Command history |
| | 41 | - Mouse modes |
| | 42 | - button strip |
| | 43 | - hot keys |
| | 44 | |
| | 45 | === Infrastructure === |
| | 46 | - Nightly builds |
| | 47 | - Preferences |
| | 48 | - Triggers |
| | 49 | - Selections |
| | 50 | - Session files |
| | 51 | - molecular data |
| | 52 | - Maybe just implement a command history rather than a full session? |
| | 53 | - Distinction between public and private API |
| | 54 | |
| | 55 | |
| | 56 | == December release == |
| | 57 | |
| | 58 | === Presentation graphics === |
| | 59 | - Transparency controllable down to individual atoms/bonds, small units of other reps |
| | 60 | - single-layer |
| | 61 | - Clipping |
| | 62 | - global hither/yon |
| | 63 | - capping of all solids: surfaces, ribbons, atoms/bonds, objects |
| | 64 | - per-model single-plane or slab |
| | 65 | - Selection highlight |
| | 66 | |
| | 67 | === CellPACK === |
| | 68 | - Open cellPACK models, fetching JSON files from web |
| | 69 | - Open collada surface files used to represent cellPACK molecules |
| | 70 | - Hierarchical collapsible list of model components |
| | 71 | - checkbuttons for display, active, etc. |
| | 72 | - Mouse hover to pop-up name of molecular component |
| | 73 | |
| | 74 | === User interface === |
| | 75 | - Simple !Selection/Action menus |
| | 76 | - Actions |
| | 77 | - Hide/show |
| | 78 | - Color |
| | 79 | - Surface |
| | 80 | - Style (atom only) |
| | 81 | - Delete |
| | 82 | - Selections |
| | 83 | - By model/chain |
| | 84 | - By structure (ions, ligand, secondary structure, etc.) |
| | 85 | - Operations (clear, invert all models, invert selected models, select all) |
| | 86 | - Rapid Access (file history in particular) |
| | 87 | - Hierarchical model panel |
| | 88 | - Active/shown checkboxes |
| | 89 | - Action buttons |
| | 90 | - Full side view (clipping planes) |
| | 91 | - Mouse selection |
| | 92 | |
| | 93 | === Infrastructure === |
| | 94 | - Essential commands, make a list with command syntax |
| | 95 | - Command documentation |
| | 96 | - Full atomspecs |
| | 97 | |
| | 98 | |
| | 99 | == Highly desirable == |
| | 100 | |
| | 101 | === Graphics and tools === |
| | 102 | - Smart molecule display |
| | 103 | - Transparency correctly rendered multiple-layer, multiple models |
| | 104 | - Color by atom/res attribute (e.g. hydrophobicity)*, geometry (e.g. radial), or volume data value (e.g. density, electrostatic potential)* |
| | 105 | - H-bonds* |
| | 106 | - Dashed and dotted pseudobonds (cylinders as well as lines) |
| | 107 | - Isosurface smoothing |
| | 108 | - Easily hide smaller surface components (like hide dust) |
| | 109 | - Geometric objects |
| | 110 | - structure-derived (best-fit planes, axes, ellipsoids, etc.)* |
| | 111 | - arbitrary (3D arrows, planes to cast shadows upon, etc.) |
| | 112 | - Scenes (so that one doesn't have to have a session for each figure panel) |
| | 113 | - Background color gradient |
| | 114 | - Other sectioning (e.g. cut octant, spherical clipping, etc.) |
| | 115 | - 3D labels |
| | 116 | - 2D labels and arrows of adjustable color/size, interactive repositioning |
| | 117 | - Color key (specialized 2D annotation) |
| | 118 | |
| | 119 | === CellPACK === |
| | 120 | - Geometric selection eg drag-select and select-within-shape |
| | 121 | |
| | 122 | === User interface === |
| | 123 | - Actions |
| | 124 | - Style |
| | 125 | - ribbon |
| | 126 | - surface |
| | 127 | - Label |
| | 128 | - Selections |
| | 129 | - By residue type or category/atom element |
| | 130 | - By chemistry (functional groups, atom types, residue properties) |
| | 131 | - Appearance (transparency and material) |
| | 132 | - Export in different formats (PDB, volume format, graphics format, etc) |
| | 133 | - Improved toolshed interface |
| | 134 | |
| | 135 | === Infrastructure === |
| | 136 | - Reliable operation on Linux |
| | 137 | - Application icon |
| | 138 | - API documentation |
| | 139 | |
| | 140 | == Would be nice == |
| | 141 | |
| | 142 | === Graphics and tools === |
| | 143 | - Ribbons fully integrated with pipes and planks |
| | 144 | - (alternative ways of "cartooning" the secondary structure elements) |
| | 145 | - Tubes (could be a sub-option of ribbons) |
| | 146 | - Continuous fade between residue ribbon segments instead of abrupt |
| | 147 | - Ring fill, aromaticity and bond multiplicity displays |
| | 148 | - (e.g. two lines or two sticks for double bonds) |
| | 149 | - Option to show solvent-accessible vs. solvent-excluded, or both |
| | 150 | - Ways to control and smooth boundary of displayed patch, maybe drawing an outline with mouse or choosing individual triangles to hide? |
| | 151 | - Individual surface triangles? |
| | 152 | - Abstracted nucleotides |
| | 153 | - slabs, lollipops, ladder rungs |
| | 154 | - need better default than in Chimera1 |
| | 155 | - Per-model silhouette |
| | 156 | - Custom silhouette |
| | 157 | - draw outline in 2D with mouse, regular geometric (e.g. circular) and maybe even free-form with smoothing? |
| | 158 | - other ways to emphasize area of interest within an outline |
| | 159 | - making stuff outside it transparent, faded, or blurred |
| | 160 | - Some kind of shininess control and/or ability to use different material properties for different objects |
| | 161 | - "Smart" clipping (keeping objects whole, e.g. multiscale subunits not sliced even if plane goes through them) |
| | 162 | - Interactively adjustable light positions |
| | 163 | - Lighting contrast slider |
| | 164 | - Background images |
| | 165 | - Publication presets? hard to decide because there are so many potentially useful combinations of styles and lighting |
| | 166 | - Clashes* |
| | 167 | - (find contacts also important for coloring interaction patches of surfaces*) |
| | 168 | |
| | 169 | === User interface === |
| | 170 | - Stereo and orthographic camera modes |
| | 171 | - RFE / bug report dialogs |
| | 172 | - Chimera 1 -> 2 session conversion |
| | 173 | |
| | 174 | |
| | 175 | == Eventually == |
| | 176 | |
| | 177 | === Unsorted === |
| | 178 | - Morphing, trajectory playback* |
| | 179 | - Animation commands (frame-argument) |
| | 180 | - Animation GUI (timeline) |
| | 181 | - Show multiple frames of a trajectory simultaneously |
| | 182 | - Windows app |
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