Changes between Version 86 and Version 87 of Needed Command Functionality

Timestamp:

Jun 8, 2015, 2:27:55 PM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -2 +2 @@
 Chimera2 command functionality needed for early release(s) based on [[EarlyReleaseRequirements]].
 
-This is somewhat high-level; more detailed guidelines and examples are in [http://www.cgl.ucsf.edu/home/meng/chi2/command-structure.html Chimera2 Command-Structure Thoughts].
+This is somewhat high-level; more detailed guidelines and examples are in [http://www.cgl.ucsf.edu/home/meng/chi2/command-structure.html Chimera2 Command-Structure Thoughts].  See also manpage mockups: 
+[http://www.cgl.ucsf.edu/home/meng/chi2/frame_atomspec2.html atomspec],
+[http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface],
+[http://www.cgl.ucsf.edu/home/meng/chi2/vcolor.html vcolor] (color-by-value),
+[http://www.cgl.ucsf.edu/home/meng/chi2/color.html color] (ommibus including color-by-value)
+
 
 == Late summer release ==
@@ -20 +25 @@
 * '''surface''' solvent-excluded molecular surface
   - see [[SurfaceCategories]] discussion of categories and command design
-  - see [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface mockup] based on subsequent discussion
+  - see [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface command mockup] based on subsequent discussion
 * '''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 these will be used frequently); styles for this release:
   - atom/bond '''stick, bs, sphere''' (and '''line'''?)
@@ -29 +34 @@
   - each style could have sub-options (''e.g.'' stick radius), or if it's too complicated to include them in the '''style''' command, they could be adjusted with '''setattr'''
   - see [http://www.cgl.ucsf.edu/home/meng/chi2/command-structure.html#examples command examples] for more detailed thoughts
-* '''color''' (leaving color-by-attr as in '''rangecolor''', color-by-scalar-field as in '''scolor''', and '''rainbow''' for later and separate from '''color''')
+* '''color''' (leaving color-by-attr as in '''rangecolor''', color-by-scalar-field as in '''scolor''', and '''rainbow''' for later)
+  - just the first usage with single colorname in the [http://www.cgl.ucsf.edu/home/meng/chi2/color.html color command mockup]
 * '''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
@@ -85 +91 @@
 * '''scolor''' or equivalent for color-by-scalar (radial, volume value, ''etc.'') 
   - logical to merge '''rangecolor''' and '''scolor''', maybe also '''rainbow''', but what's a good name? ...'''rendervalue''' (which could include worms/radii by attr), '''colorscale''', many other possibilities... see [http://www.cgl.ucsf.edu/home/meng/chi2/vcolor.html color-by-value command mockup]
-  - color-by-scalar might only apply to surfaces and atoms, unless we want cartoons to show residue values derived from the substituent atomic values
+  - or, even merge with main color command, see [http://www.cgl.ucsf.edu/home/meng/chi2/color.html omnibus color command mockup]
 * '''findhbond'''
   - consider option to find salt bridges only