Changes between Version 55 and Version 56 of Needed Command Functionality

Timestamp:

May 14, 2015, 1:51:45 PM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -8 +8 @@
 Initial versions (not necessarily full implementations, could be partial) of:
 * '''open''' (suggest same general syntax as Chimera1, possibly adjusting prefixes; covers both local files and web-fetch)
+  - for this release: PDB, PDB/mmCIF, density maps
 * '''display''', '''modeldisplay''' (suggest replacing with '''show/hide''')
   - this could control pseudobonds indirectly if they are hidden automatically when endpoint atoms are hidden, but we may want to make it act on them directly, or else '''setattr''' (see below) might be the only way
 * '''ribbon''' (suggest replacing with '''cartoon''' and including spline, path smoothing, whether backbone atoms can be shown, and any other whole-chain parameters as options to this command)
   - see [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup]
-  - for this release, just ribbons (not cylinders or worms)
+  - for this release, just ribbons (not cylinders or worm-by-attr)
 * '''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
 * '''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 '''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 as in '''rangecolor''' and color-by-scalar-field as in '''scolor''' separate; '''rainbow''' might be merged with those two)
+  - 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 at least '''smooth''' and '''edged''' with default scaling; '''tube''' should actually be easier although not listed until the '''Would be nice''' section)
+* '''color''' (leaving color-by-attr as in '''rangecolor''', color-by-scalar-field as in '''scolor''', and '''rainbow''' for later and separate from '''color''')
 * '''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
@@ -47 +48 @@
 * '''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)
+* single-layer transparency ('''set''' or other command control)
 * '''freeze''' or something like that to control model activation for motion (in Chimera1, '''freeze''' is something different)
 
 Expanded functionality of existing commands:
 * '''open''' (including fetch) cellPACK
+* '''select''' all, clear, invert
 
 Command accoutrements:
@@ -80 +82 @@
 * '''save/export''' PDB, volume data, ''etc.'' (question: what is the distinction between save and export?  I don't understand how various programs divide output into these categories)
 
+Expanded functionality of existing commands:
+* '''style''' options for pseudobonds '''dashed, dotted, dotdash''', with 3D versions preferred over lines
+
 Command accoutrements:
 * more built-in specs like functional groups, amino acid categories, element symbols, ''etc.''
@@ -91 +96 @@
 * '''surface''' provisions for multiple surfaces on same atoms, including SAS and/or SES
 
+Expanded functionality of existing commands:
+* atoms/bonds ring fill, aromaticity, and bond multiplicity display (sub-options of '''style stick''' and/or settable with '''setattr''')
+* '''style''' option for cartoons, '''tube''' (similar to our current rounded licorice)
+
 == Eventually ==
 * motion-scripting or other frame-argument commands (see [http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands Chimera1 movie-related commands])