| | 1 | = Presentation Graphics Features Wishlist = |
| | 2 | |
| | 3 | == Required == |
| | 4 | - sessions (required because one needs to save state for any pub figure) |
| | 5 | - transparency controllable down to individual atoms/bonds, small units of other reps |
| | 6 | - single-layer |
| | 7 | - correctly rendered multiple-layer, multiple models |
| | 8 | - ribbons |
| | 9 | - cardinal spline option, at least for loops (non-alpha,non-beta) |
| | 10 | - molecular surface |
| | 11 | - molecular surface categories* (I think the default should have a separate "main" for each chain ID) |
| | 12 | - easily hide smaller bits (like "surf visiblePatches N") |
| | 13 | - clipping |
| | 14 | - global hither/yon |
| | 15 | - capping of all solids: surfaces, ribbons, atoms/bonds, objects |
| | 16 | - per-model single-plane or slab |
| | 17 | - smoothness control (vertex density, subdivision) |
| | 18 | - pseudobonds |
| | 19 | - metal complexation |
| | 20 | - distance monitor |
| | 21 | |
| | 22 | - '''Done?''' |
| | 23 | - atom/bond styles: sticks, bs, sphere, individually controllable |
| | 24 | - show/hide controllable down to individual atoms, small units of other reps |
| | 25 | - coloring controllable down to individual atoms, small units of other reps |
| | 26 | - silhouettes |
| | 27 | - adjustable background color |
| | 28 | - interactive shadows |
| | 29 | - lighting options - ambient occlusion, ambient-only, N-point |
| | 30 | - supersampling |
| | 31 | |
| | 32 | == Highly desirable == |
| | 33 | - scenes (so that one doesn't have to have a session for each figure panel) |
| | 34 | - fully integrated with pipes and planks |
| | 35 | - (alternative ways of "cartooning" the secondary structure elements) |
| | 36 | - tubes (could be a sub-option of ribbons) |
| | 37 | - abstracted nucleotides - slabs, lollipops, ladder rungs |
| | 38 | - (need better default than in Chimera1) |
| | 39 | - per-model silhouette |
| | 40 | - custom silhouette |
| | 41 | - draw outline in 2D with mouse, regular geometric (e.g. circular) and maybe even free-form with smoothing? |
| | 42 | - molecular surface and volume isosurface styles: solid, mesh |
| | 43 | - easily hide smaller components (like hide dust) |
| | 44 | - background color gradient, images |
| | 45 | - depth cueing (adjustable color, amount) |
| | 46 | - interactively adjustable light positions |
| | 47 | - lighting contrast slider |
| | 48 | - other sectioning (e.g. cut octant, spherical clipping, etc.) |
| | 49 | - 2D labels and arrows of adjustable color/size, interactive repositioning |
| | 50 | - color key (specialized 2D annotation) |
| | 51 | - geometric objects |
| | 52 | - structure-derived (best-fit planes, axes, ellipsoids, etc.)* |
| | 53 | - arbitrary (3D arrows, planes to cast shadows upon, etc.) |
| | 54 | - color by atom/res attribute (e.g. hydrophobicity)*, geometry (e.g. radial), or volume data value (e.g. density, electrostatic potential)* |
| | 55 | - H-bonds and clashes* |
| | 56 | - (find contacts also important for coloring interaction patches of surfaces*) |
| | 57 | |
| | 58 | - morphing, trajectory playback* |
| | 59 | - animation commands (frame-argument) |
| | 60 | |
| | 61 | - '''Done?''' |
| | 62 | - set of built-in colors (as opposed to giving hex code or RGBs only) |
| | 63 | |
| | 64 | == Would be nice == |
| | 65 | - individual surface triangles? |
| | 66 | - continuous fade between residue ribbon segments instead of abrupt |
| | 67 | - ring fill, aromaticity and bond multiplicity displays |
| | 68 | - (e.g. two lines or two sticks for double bonds) |
| | 69 | - other ways to emphasize area of interest within an outline |
| | 70 | - making stuff outside it transparent, faded, or blurred |
| | 71 | - option to show solvent-accessible vs. solvent-excluded, or both |
| | 72 | - ways to control and smooth boundary of displayed patch, maybe drawing an outline with mouse or choosing individual triangles to hide? |
| | 73 | - some kind of shininess control and/or ability to use different material properties for different objects |
| | 74 | - "smart" clipping (keeping objects whole, e.g. multiscale subunits not sliced even if plane goes through them) |
| | 75 | - publication presets? hard to decide because there are so many potentially useful combinations of styles and lighting |
| | 76 | |
| | 77 | - animation GUI (timeline) |
| | 78 | - show multiple frames of a trajectory simultaneously |
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