Changes between Version 72 and Version 73 of Needed Command Functionality

Timestamp:

May 18, 2015, 2:41:35 PM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -82 +82 @@
   - color-by-scalar might only apply to surfaces and atoms, unless we want cartoons to show residue values derived from the substituent atomic values
 * '''findhbond'''
+  - consider option to find salt bridges only
 * '''define''' geometric objects based on atomic coordinates: axes, planes, centroids, ellipsoids
 * '''shape''' or other way of defining geometric objects arbitrarily
@@ -111 +112 @@
   - need better defaults than in Chimera1, at least for smart display
 * '''findclash''' (also needed for coloring surface interaction patches)
-  - should be easier than in Chimera1 to use contact defaults in command (the overall defaults are clash defaults)
+  - consider facilitating the use of contact defaults (in Chimera1, the overall defaults are the clash defaults, so to use the GUI's contact defaults you have to look up the two values in the documentation and specify them individually in the command)
 
 Expanded functionality of existing commands:
+* '''open''' Chimera1 sessions (session conversion)
 * '''preset''' publication options 
 * '''cartoon''' options for pipes and planks
@@ -122 +124 @@
 * '''surface''' 
  - provisions for multiple surfaces on same atoms, including SAS and/or SES
- - patch boundary-smoothing, could be keyword '''smoothBorders''' as in the [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface manpage mockup]; also mentioned are individual triangle-hiding or hand-drawn boundaries, not sure whether/how that might relate to commands
+ - patch boundary-smoothing, see '''smoothBorders''' in the [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface manpage mockup]
 * atoms/bonds ring fill, aromaticity, and bond multiplicity display (sub-options of '''style stick''' and/or settable with '''setattr'''; could also apply to '''style line''', but do we still need that style?)
 * smart clipping, leaving individual objects such as multiscale surfaces whole
  - potentially options of '''clip, mclip'''
  - in Chimera1, certain things are already only wholly selectable (surface pieces, ''etc.''), but if we become able to select subparts/triangles within surfaces, it could also be an option of '''select'''
-* '''setattr''' (or other command) individual attributes: shininess (and/or '''set''' global shininess?), other material properties, per-model silhouettes (remove silhouettes from global settings?)
-* '''set''' (or other command) global parameters: background images, contrast
+* '''set''' (or other command) global settings: background images, lighting contrast, camera modes (orthographic, stereo)
+* '''setattr''' (or other command) attributes: individual shininess (and/or '''set''' global shininess?), other individual material properties, per-model silhouettes (remove silhouettes from global settings?)
 
 GUI-only, or do we need commands?
 * interactively adjustable light positions
+* for surface patch boundary smoothing, individual triangle-hiding or hand-drawn boundaries
 * hand-drawn or 2D-shape custom silhouettes (2D outlines? perhaps could be an option of '''2dlabels''')... also ties in with the fancy-shaped selection in the '''Highly desirable''' section
 
 == Eventually ==
+* '''morph'''
+  - atoms/bonds
+  - maps
+* '''coordset'''-like trajectory playback but also the ability to show more than one frame at a time
 * motion-scripting or other frame-argument commands (see [http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands Chimera1 movie-related commands])
+  - I'm hoping for saved positions and commands for traversing them: '''savepos/reset/fly'''
+  - although Chimera1 has scenes, it doesn't have command controls analogous to the above for fully scripting timeline playback; our designs for '''transition''' and '''animate''' commands were never implemented