Changes between Version 3 and Version 4 of PresentationGraphics

Timestamp:

Apr 9, 2015, 3:12:18 PM (11 years ago)

Author:

Conrad Huang

Comment:

--

PresentationGraphics

@@ -1 +1 @@
 = Presentation Graphics Features Wishlist =
+
+asterisk = requires some analysis code
 
 == Required ==
@@ -5 +7 @@
  - sessions (required because one needs to save state for any pub figure)
  - ribbons
-   - cardinal spline option, at least for loops (non-alpha,non-beta)
+   - 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
@@ -16 +19 @@
  - transparency controllable down to individual atoms/bonds, small units of other reps
    - single-layer
-   - correctly rendered multiple-layer, multiple models
  - clipping
    - global hither/yon
    - capping of all solids: surfaces, ribbons, atoms/bonds, objects
    - per-model single-plane or slab
+ - selection highlight
 
-- '''Done?'''
+- '''Partially done?  More clean up.'''
   - atom/bond styles: sticks, bs, sphere, individually controllable
   - show/hide controllable down to individual atoms, small units of other reps
@@ -31 +34 @@
   - lighting options - ambient occlusion, ambient-only, N-point
   - supersampling
+  - volume isosurfaces
+  - depth cueing (want adjustable color, amount)
 
 == Highly desirable ==
+- 3D labels
+- transparency correctly rendered multiple-layer, multiple models
+- isosurface smoothing
 - scenes (so that one doesn't have to have a session for each figure panel)
-- fully integrated with pipes and planks 
+- easily hide smaller surface components (like hide dust)
+- background color gradient
+- other sectioning (e.g. cut octant, spherical clipping, etc.)
+- 2D labels and arrows of adjustable color/size, interactive repositioning
+- color key (specialized 2D annotation)
+- geometric objects 
+  - structure-derived (best-fit planes, axes, ellipsoids, etc.)*
+  - arbitrary (3D arrows, planes to cast shadows upon, etc.)
+- 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)
+
+- '''Done?'''
+  - set of built-in colors (as opposed to giving hex code or RGBs only)
+  - molecular surface and volume isosurface styles: solid, mesh
+
+== Would be nice ==
+- clashes*
+  - (find contacts also important for coloring interaction patches of surfaces*)
+- interactively adjustable light positions
+- lighting contrast slider
+- background images
+- ribbons fully integrated with pipes and planks 
   - (alternative ways of "cartooning" the secondary structure elements)
 - tubes (could be a sub-option of ribbons)
@@ -42 +72 @@
 - custom silhouette
   - draw outline in 2D with mouse, regular geometric (e.g. circular) and maybe even free-form with smoothing?
-- molecular surface and volume isosurface styles: solid, mesh
-  - easily hide smaller components (like hide dust)
-- background color gradient, images
-- depth cueing (adjustable color, amount)
-- interactively adjustable light positions
-- lighting contrast slider
-- other sectioning (e.g. cut octant, spherical clipping, etc.)
-- 2D labels and arrows of adjustable color/size, interactive repositioning
-- color key (specialized 2D annotation)
-- geometric objects 
-  - structure-derived (best-fit planes, axes, ellipsoids, etc.)*
-  - arbitrary (3D arrows, planes to cast shadows upon, etc.)
-- color by atom/res attribute (e.g. hydrophobicity)*, geometry (e.g. radial), or volume data value (e.g. density, electrostatic potential)*
-- H-bonds and clashes*
-  - (find contacts also important for coloring interaction patches of surfaces*)
-
-- morphing, trajectory playback*
-- animation commands (frame-argument)
-
-- '''Done?'''
-- set of built-in colors (as opposed to giving hex code or RGBs only)
-
-== Would be nice ==
+  - other ways to emphasize area of interest within an outline 
+    - making stuff outside it transparent, faded, or blurred
 - individual surface triangles?
 - 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)
-- other ways to emphasize area of interest within an outline 
-  - making stuff outside it transparent, faded, or blurred
 - 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?
@@ -77 +84 @@
 - publication presets?  hard to decide because there are so many potentially useful combinations of styles and lighting
 
+== Eventually ==
+- morphing, trajectory playback*
+- animation commands (frame-argument)
 - animation GUI (timeline)
 - show multiple frames of a trajectory simultaneously