Changes between Version 62 and Version 63 of Needed Command Functionality

Timestamp:

May 18, 2015, 10:29:36 AM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -13 +13 @@
 * '''ribbon''' (suggest replacing with '''cartoon''' and including spline, path-smoothing, 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 worm-by-attr)
+  - for this release, just ribbons (not pipes/cylinders or worm-by-attr)
 * '''surface''' solvent-excluded molecular surface
   - see [[SurfaceCategories]] discussion of categories and command design
@@ -45 +45 @@
 * set of built-in color names
 * built-in specs '''solvent, ions, ligand, main, helix, strand, coil''' (needed for molecular surface and ribbon anyway, might as well make them available for command-line use)
+* basic hierarchical atomspecs (see [http://www.cgl.ucsf.edu/home/meng/chi2/frameatom_spec2.html Chimera2 atomspec writeup])
 
 == December release ==
@@ -50 +51 @@
 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''')
+ - single-layer transparency ('''set''' or other command control)
 * '''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 an option in '''clip''' and/or '''mclip''')
-* single-layer transparency ('''set''' or other command control)
-* '''freeze''' or some other command to control model activation for motion (in Chimera1, '''freeze''' is something different)
+ - capping of all solid objects, including surfaces, cartoons, atoms/bonds ('''set''' if global, '''setattr''' if per-object; could also be an option in '''clip''' and/or '''mclip''')
+* pseudobonds that could be intermodel (implying need for '''distance''')
+* '''active/~active, freeze/~freeze''' or some other command to control model activation for motion (in Chimera1, '''freeze''' is something different)
 * '''help''' to bring up command documentation
 
 Expanded functionality of existing commands:
-* '''open''' (including fetch) cellPACK
+* '''open''' (including fetch) cellPACK, which would elicit interface for exploring hierarchy
 * '''select''' all, clear, invert
 
 Command accoutrements:
-* more built-in specs like '''protein, nucleic acid''',''etc.''
+* command documentation
 * full atomspecs (see [http://www.cgl.ucsf.edu/home/meng/chi2/frameatom_spec2.html Chimera2 atomspec writeup])
-* translation of menu actions into commands (if needed for full logging... maybe it's not?)
+* translation of menu actions into commands (if needed for full logging and replay... maybe it's not?)
 
 == Highly desirable ==
@@ -86 +87 @@
 * '''2dlabels'''
 * '''colorkey'''
-* adjustable material properties ('''setattr''' or other)
-* background color-gradient ('''set''' or top-level '''background''' command)
-* multiple-layer transparency ('''set''' or other command control)
 * '''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 (and maybe bonds) '''dottedStick, dashedStick, dotdashStick''' and I guess '''dottedLine, dashedLine, dotdashLine''' (but do we even need the lines any more?)
+* '''style''' options for pseudobonds: dotted and dashed sticks, dotted and dashed lines (but do we really need the latter any more?)
+* '''set''' (or other command) global settings: background color gradient, multiple-layer transparency
+* '''setattr''' (or other command) attributes: material properties
 
 Command accoutrements:
-* more built-in specs like functional groups, amino acid categories, element symbols, ''etc.''
+* more built-in specs like '''protein, nucleic acid,''' functional groups, amino acid categories, element symbols, ''etc.''
 
 == Would be nice ==