Changes between Version 131 and Version 132 of Needed Command Functionality

Timestamp:

Dec 10, 2015, 3:29:13 PM (10 years ago)

Author:

Eric Pettersen

Comment:

--

Needed Command Functionality

@@ -12 +12 @@
 Potential renaming of Chimera1 commands (up for discussion):
 - ~~Chimera1 '''freeze''' → Chimera2 '''stop'''~~ (done)
- - Nov 5 2015 Greg will add Log message to remind users of '''stop''' function if no ongoing motion
+ - ~~Nov 5 2015 Greg will add Log message to remind users of '''stop''' function if no ongoing motion
 -  ~~'''~select/select''' (model activation/deactivation) → '''freeze/~freeze'''~~
- - Nov 5 2015 decided activation concept not needed in Chimera2
+ - ~~Nov 5 2015 decided activation concept not needed in Chimera2
 - ~~'''window, focus''' → '''view ''spec'' '''~~ (done)
 - ~~'''windowsize''' → '''window'''~~
- - Nov 5 2015 deemed unnecessary now that it can be truncated (since the '''window''' command is not present)
+ - ~~Nov 5 2015 deemed unnecessary now that it can be truncated (since the '''window''' command is not present)
 - ~~'''scale''' → '''zoom'''~~ (done)
 - ~~'''display/modeldisplay''' → '''show/hide'''
  - Nov 2 2015 agreed to proceed with this, with '''~show''' as an undocumented alias to '''hide'''
-- '''alias''' (target-defining function) → '''namespec''' (previously agreed upon)
- - Nov 5 2015 for the other (command-defining) function of '''alias''', agreed to change syntax for listing and deleting aliases, and to use analogous approach for other commands that also allow the user to assign names to definitions ('''namespec''', '''colordef''', ''etc.''...'''view''' is already that way)
-    - '''alias''' → '''alias list'''
-    - '''~alias ''name''''' → '''alias delete (''name''|all)'''
+- '''namespec''' not yet implemented
+ - ~~Nov 5 2015 for the other (command-defining) function of '''alias''', agreed to change syntax for listing and deleting aliases, and to use analogous approach for other commands that also allow the user to assign names to definitions ('''namespec''', '''colordef''', ''etc.''...'''view''' is already that way)
+    - ~~'''alias''' → '''alias list'''
+    - ~~'''~alias ''name''''' → '''alias delete (''name''|all)'''
 - ~~'''2dlabels''' → '''title'''~~ (done)
-- ~~'''ribbon''' → '''cartoon'''~~ (done but we still have '''ribbon''' as a synonym)
+- ~~'''ribbon''' → '''cartoon''' (done but we still have '''ribbon''' as a synonym)
 
 == Late summer release ==
 
 Initial versions (not necessarily full implementations) of:
-* '''open''' (both local files and web-fetch)
-  - for this release: PDB, PDB/mmCIF, density maps, sessions
-  - as of Nov 2 2015 done for the above except sessions
-  - prefixes (''e.g.'' '''pdb:''' should allow opening file with non-standard suffix as that format; currently only treats the string as an ID code)
-  - Nov 5 2015 intend to add keywords '''from''' to specify database for web fetch and '''format''' which could be useful for both fetch and local files, and possibly other keywords; retain colon syntax as alternative
+* ~~'''open''' (both local files and web-fetch)
+  - ~~for this release: PDB, PDB/mmCIF, density maps, sessions
+  - ~~add keywords '''from''' to specify database for web fetch and '''format''' which could be useful for both fetch and local files, and possibly other keywords; retain colon syntax as alternative
 * ~~'''close'''~~ (done for models; might want to add '''session''' and/or '''all''' keywords later)
 * ~~'''exit, quit''' or equivalent~~ (done)
 * ~~something like Chimera1 '''focus''' and/or '''window''' (rename as '''view''')~~ (done)
-* '''display''', '''modeldisplay''' (plan to replace with '''show/hide''')
-  - as of Nov 2 2015 implemented as '''display''' and its options 
-  - Nov 5 2015 some discussion as to whether a show-only option (like Chimera1 '''show''') is possible; there is an undocumented '''only''' option but EM and TG think it may be too confusing in combination with the other options of the command
+* ~~'''display''', '''modeldisplay''' (plan to replace with '''show/hide''')
+  - ~~as of Nov 2 2015 implemented as '''display''' and its options 
+  - ~~Nov 5 2015 some discussion as to whether a show-only option (like Chimera1 '''show''') is possible; there is an undocumented '''only''' option but EM and TG think it may be too confusing in combination with the other options of the command
 * '''cartoon''' including spline, path-smoothing, and any other whole-chain parameters as options
   - see [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup]
-  - for this release, just ribbons (not pipes/cylinders or worm-by-attr)
-  - as of Nov 2 2015 the above is done but no controls for width, thickness, cross-sectional shape (would this be in '''cartoon''' or '''style'''?)
+  - ~~for this release, just ribbons (not pipes/cylinders or worm-by-attr)
+  - controls for width, thickness, cross-sectional shape (would this be in '''cartoon''' or '''style'''?)
   - Nov 5 2015 tether options have not been separated out (still '''tetherShape''' etc. options of '''cartoon''' instead of '''shape''' etc. options of '''cartoon tether''')
 * ~~'''surface''' solvent-excluded molecular surface~~ (done)
@@ -60 +58 @@
 
 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)~~ (done, some via '''set''', some via other commands such as '''lighting''')
-  - 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) (done, some via '''set''', some via other commands such as '''lighting''')
 * '''setattr''' attribute values
   - need some way for the user to look up the names and possible values of attributes
 
 For this release, GUI-only or commands? (eventually they should be commands)
-* '''select''' (including up/down) see [http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#expandselect Chimera1 selection cascades]
-  - as of Nov 2 2015 a good '''select''' command but hierarchy is very limited compared to Chimera1 (presumably will be expanded later) and command doesn't include up/down options
+* ~~'''select''' (including up/down) see [http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html#expandselect Chimera1 selection cascades]
+  - not full hierarchy yet
 * '''save session''' with restore covered by '''open''', or '''session (save|restore)'''
 * ~~'''save image''' with supersampling option~~ (done)