Changes between Version 52 and Version 53 of Needed Command Functionality

Timestamp:

May 14, 2015, 12:42:50 PM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -13 +13 @@
   - for this release, just ribbons (not cylinders or worms)
 * '''surface''' 
-  - see [[SurfaceCategories]] discussion of categories and command design on wiki
+  - 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
 * '''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 rounded and edged with default scaling, and rounded with licorice scaling, i.e. thin tube)
+  - 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)
 * '''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])
@@ -34 +34 @@
 * decide on what kinds of colorspecs are allowed, ''e.g.'' can color names include spaces?
 * set of built-in color names
+* built-in specs '''solvent, ions, ligand, main''' (needed for molecular surface calculations anyway, might as well make them available for command-line use)
 
 == December release ==
@@ -39 +40 @@
 The following functionality is listed for the December release, but not necessarily as commands:
 * '''transparency''' (similar to '''color'''; takes care of individual settings, whereas '''set''' or another command would be used for related global parameters)
+* pseudobonds that could be intermodel (implying need for '''distance''' and maybe '''hbond, findclash''' functionality)
+* '''clip''', '''section''', '''thickness''' (suggest combining into single command to control global clipping, say '''clip''' or '''gclip''')
+* '''mclip''' per-model clipping, plane or slab
+* 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)
-* '''clip''', '''section''', '''thickness''' (suggest combining into single command to control global clipping, say '''clip''' or '''gclip''')
-* '''mclip''' per-model clipping
-* '''distance''' pseudobonds that could be intermodel
-* '''sop cap''' or equivalent (unless global options in '''clip''' would suffice)
-* single-layer transparency ('''set''' or other command control)
 
 Command accoutrements: