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Changes between Version 121 and Version 122 of Needed Command Functionality

Timestamp:: Nov 6, 2015, 1:49:29 PM (10 years ago)
Author:: Elaine Meng
Comment:: --

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: Added
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: Modified

Needed Command Functionality

-              v121
+              v122
  - 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 Chimear2
+ - Nov 5 2015 decided activation concept not needed in Chimera2
 - ~~'''window, focus''' → '''view ''spec'' '''~~ (done)
 - ~~'''windowsize''' → '''window'''~~
 …
 Initial versions (not necessarily full implementations) of:
 * '''open''' (suggest same general syntax as Chimera1, possibly adjusting prefixes; covers both local files and web-fetch)
+* '''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 useful for both fetch and local files, and possibly other keywords; retain colon syntax as alternative
+  - 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
 * ~~'''close'''~~ (done for models; might want to add '''session''' and/or '''all''' keywords later)
 * ~~'''exit, quit''' or equivalent~~ (done)
 …
   - 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 partial implementation: protein only, no controls for style (width, thickness, cross-sectional shape; would this be in '''cartoon''' or '''style'''?)
 * '''surface''' solvent-excluded molecular surface
+  - 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'''?)
+* ~~'''surface''' solvent-excluded molecular surface~~ (done)
   - see [[SurfaceCategories]] discussion of categories and command design
   - see [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface command mockup] based on subsequent discussion
+  - as of Nov 2 2015 a fairly extensive '''surface''' implementation including calculation options, showing/hiding down to the level of atomic patches
+  - EM remaining thoughts:
+    - do we want to add '''~surface''' as synonym for '''surface hide'''?
+    - do we need mesh or dot options, and if so, via what command ('''surface''' or '''style''' or other?)
+* '''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'''~~ (implemented via '''style'''; do we need a '''line''' style?)
+  - pseudobond '''dashedStick''' (since TomG already added it; could be named something else)
+  - '''stick''' and '''line''' (if we even have the latter) would apply to both atoms/bonds and pseudobonds
+  - surface (volume isosurface and molecular surface) '''solid, mesh'''
+  - a default style or a few possibilities for ribbons/cartoons (say '''smooth''' and '''edged''', maybe '''flat''', with default scaling; '''tube''' should be easier to implement than those, even though it's down in the '''Would be nice''' section)
+  - 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
+  - Nov 5 2015 plan to add '''~surface''' as undocumented alias to '''surface hide''', if possible
 * ~~'''color''' (just the first usage with single colorname in the [http://www.cgl.ucsf.edu/home/meng/chi2/color.html color command mockup]~~ (done)
   - leaving color-by-attr as in '''rangecolor''', color-by-scalar-field as in '''scolor''', and '''rainbow''' for later
 * '''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])
+  - I ''think'' it's done, in that '''volume''' has been completely ported over from Chimera1
+* 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
+  - Nov 5 2015 '''volume''' has been ported over from Chimera1 but Tom G will check over it to see which parts are functional (we know at least a few things related to commas are problematic in Chimera2)
+* some way to adjust subdivision/smoothness
+  - Nov 5 2015 done for atoms/bonds ('''set subdivision''') but not cartoons
+  - done for molecular surfaces; '''surface''' has grid-spacing, resolution options
 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)
+  - 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
-  - as of Nov 2 2015 at least some of this is 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
 …
   - 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
 * '''save session''' with restore covered by '''open''', or '''session (save|restore)'''
 * '''save image''' with supersampling option
+* ~~'''save image''' with supersampling option~~ (done)
 Command accoutrements:
 …
 Again listed but not necessarily as commands:
+* '''repr''', '''ribrepr''', '''ribscale''', '''surfrepr''' (maybe consolidate into '''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):
+  - ~~atom/bond '''stick, bs, sphere'''~~ (implemented via '''style'''; do we need a '''line''' or '''wire'''?)
+  - pseudobond '''dashedStick''' (since TomG already added it; could be named something else)
+  - '''stick''' and '''line''' (if we even have the latter) would apply to both atoms/bonds and pseudobonds
+  - surface (volume isosurface and molecular surface) '''solid, mesh'''
+  - a default style or a few possibilities for ribbons/cartoons (say '''smooth''' and '''edged''', maybe '''flat''', with default scaling; '''tube''' should be easier to implement than those, even though it's down in the '''Would be nice''' section)
+  - 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
+  - Nov 5 2015 decided to leave on the table, revisit when we figure out what comprises a cartoon style and have more of them to play with
 * smart molecule display
   - IMO, this implies the need for '''preset''' with at least two interactive options: one with all atoms shown and one similar to the smart display; I'd vote for a third one with molecular surface(s) colored to match the corresponding chain's ribbon, possibly transparent
 * color-by-attr as in '''rangecolor''', color-by-scalar-field as in '''scolor''', and color sequentially as in '''rainbow'''
+   - EM: I favor merging with main '''color''' command, see [http://www.cgl.ucsf.edu/home/meng/chi2/color.html omnibus color command mockup] ( [http://www.cgl.ucsf.edu/home/meng/chi2/vcolor.html color-by-value command mockup] is less refined, I stopped working on it)
+   - merge into main'''color''' command, see [http://www.cgl.ucsf.edu/home/meng/chi2/color.html color command mockup]
+   - need to add more palettes, including color-blind-friendly
   - '''defattr''' would be useful for reading in custom attributes
 * '''findhbond'''
 …
  - patch boundary-smoothing, see '''smoothBorders''' in the [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface command mockup]
   - as of Nov 2 2015 done-ish, '''sharpBoundaries''' option fulfills similar role
+* surface '''style''' option '''mesh'''
 * 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