Changes between Version 66 and Version 67 of Needed Command Functionality

Timestamp:

May 18, 2015, 11:53:06 AM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -104 +104 @@
 == Would be nice ==
 
-Again listed but not necessarily as commands: 
+Again listed but not necessarily as commands:
+* '''preset''' publication options 
 * '''nucleotides''' base-slab, sugar-tube, and ladder 
   - need better defaults than in Chimera1, at least for smart display
+* '''findclash'''
+  - finding contacts also important for coloring surface interaction patches
 
 Expanded functionality of existing commands:
-* '''cartoon''' options for cylinders/pipes and planks (or should these be '''style''' options for existing cartoons instead? should also integrate with helix axes, ''i.e.'' the pipes=axes could be used in measurements)
- - I'm thinking cylinders could be a distinct option for helices, but that we don't really need perfectly box-shaped planks if there is an option for well-smoothed strands (like our default B spline strands in Chimera1)
-* '''style''' option for cartoons, '''tube''' (similar to our current rounded licorice)
-* '''surface''' provisions for multiple surfaces on same atoms, including SAS and/or SES
+* '''cartoon''' options for pipes and planks
+ - that's what the [[EarlyReleaseRequirements]] says, but I don't think box-shaped planks are needed (or even desirable) if there is an option for well-smoothed strands similar to our B spline strands in Chimera1; beta-sheet curvature is the rule rather than the exception
+ - cylinders (pipes) could be a distinct option for helices and should integrate with helix axes, ''i.e.'' the pipes=axes could be used in measurements
+ - see [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup]
+* cartoon '''style''' option '''tube''' (similar to our current rounded licorice)
+* '''surface''' 
+ - provisions for multiple surfaces on same atoms, including SAS and/or SES
+ - patch boundary-smoothing, could be keyword '''smoothBorders''' as in [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
 * atoms/bonds ring fill, aromaticity, and bond multiplicity display (sub-options of '''style stick''' and/or settable with '''setattr''')
+* '''setattr''' (or other command) attributes: per-model silhouettes (remove silhouettes from global settings?), material shininess (and/or '''set''' global shininess?)
+  - hand-drawn or 2D shape custom silhouettes were also mentioned, not sure whether/how they would relate to commands, or if they should be called something else (2D outlines? maybe should be an option of '''2dlabels''' instead)
+* '''set''' (or other command) global parameters: lighting contrast, light positions,