Changes between Version 84 and Version 85 of Needed Command Functionality

Timestamp:

Jun 1, 2015, 3:23:12 PM (11 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -20 +20 @@
 * '''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 manpage mockup] based on subsequent discussion
+  - see [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface 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'''?)
@@ -84 +84 @@
   - then '''defattr''' would be useful
 * '''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...
+  - 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/color.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
 * '''findhbond'''
@@ -130 +130 @@
 * '''surface''' 
  - provisions for multiple surfaces on same atoms, including SAS and/or SES
- - patch boundary-smoothing, see '''smoothBorders''' in the [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface manpage mockup]
+ - patch boundary-smoothing, see '''smoothBorders''' in the [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface 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