Changes between Version 54 and Version 55 of Needed Command Functionality

Timestamp:

May 14, 2015, 1:32:20 PM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -10 +10 @@
 * '''display''', '''modeldisplay''' (suggest replacing with '''show/hide''')
   - this could control pseudobonds indirectly if they are hidden automatically when endpoint atoms are hidden, but we may want to make it act on them directly, or else '''setattr''' (see below) might be the only way
-* '''ribbon''' (suggest replacing with '''cartoon''' and including spline, path smoothing, whether backbone atoms can be shown, and any other whole-chain parameters as options to this command; see [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup])
+* '''ribbon''' (suggest replacing with '''cartoon''' and including spline, path smoothing, whether backbone atoms can be shown, and any other whole-chain parameters as options to this command)
+  - see [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup]
   - for this release, just ribbons (not cylinders or worms)
 * '''surface''' solvent-excluded molecular surface
@@ -17 +18 @@
 * '''repr''', '''ribrepr''', '''ribscale''', '''surfrepr''' (maybe consolidate into a new '''style''' command, generalizing ribbon to cartoon as per [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup], and including pseudobonds; I'm not sure consolidation is better, however, since consolidation makes longer commands, and for such frequently used functionality we need easy-to-type commands)
   - styles for this release include atom/bond '''stick, bs, sphere'''; surface '''solid, mesh'''; and at least a default style or a few possibilities for ribbons/cartoons (I suggest '''smooth''' and '''edged''' with default scaling, and rounded with licorice scaling, i.e. thin '''tube'''; eventual pseudobond styles could include '''dashed, dotted, dotdash''', with 3D versions preferred over lines)
-* '''color''' (leaving color-by-attr '''rangecolor''' and color-by-scalar-field '''scolor''' separate; '''rainbow''' might be merged with those two)
+* '''color''' (leaving color-by-attr as in '''rangecolor''' and color-by-scalar-field as in '''scolor''' separate; '''rainbow''' might be merged with those two)
 * '''volume''' control over isosurface display (redundancy with show/hide/color etc. OK with me, but should review structure and keywords ''vs.'' the negotiable [http://www.cgl.ucsf.edu/home/meng/chi2/command-structure.html command guidelines])
 * some way to adjust subdivision/smoothness; any global setting could be covered by '''set''' (see below) and any attribute by '''setattr''', but there could also be options in '''surface''', '''volume''', '''cartoon''' and/or a top-level '''quality''' command
 
 Extremely useful catchalls that I suggest retaining as permanent commands even though there will be some redundancy:
-* '''set''' global settings; for this release: silhouettes, background color, depth-cuing amount and color, interactive shadows, lighting (ambient occlusion, ambient-only, N-point) (if many sub-options, e.g. lighting, could make a separate top-level command; also keeping a redundant but longer '''set''' command is OK with me) 
+* '''set''' global settings
+  - for this release: silhouettes, background color, depth-cuing amount and color, interactive shadows, lighting (ambient occlusion, ambient-only, N-point)
+  - if many sub-options, e.g. lighting, could make a separate top-level command; also keeping a redundant but longer '''set''' command is OK with me 
 * '''setattr''' attribute values
 
@@ -45 +48 @@
 * capping of all solid objects ('''set''' if global, '''setattr''' if per-object; could also be options in '''clip''' and/or '''mclip''')
 * single-layer transparency ('''set''' or other command control if possible to turn off)
-* '''open''' (including fetch) capability for cellPACK
 * '''freeze''' or something like that to control model activation for motion (in Chimera1, '''freeze''' is something different)
+
+Expanded functionality of existing commands:
+* '''open''' (including fetch) cellPACK
 
 Command accoutrements: