Changes between Version 65 and Version 66 of Needed Command Functionality

Timestamp:

May 18, 2015, 11:24:32 AM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -93 +93 @@
 Expanded functionality of existing commands:
 * '''style''' options for pseudobonds: dotted and dashed sticks, dotted and dashed lines (but do we really need the latter any more?)
-* fancy-shaped clipping (if global add options to '''clip''', otherwise to '''mclip''' if feasible; Chimera1 has octant stuff in '''vop''' subcommands)
-* '''volume''' isosurface smoothing, maybe '''sop hideDust''' equivalent (is this used for anything other than isosurfaces?)
+* fancy-shaped selection and clipping (if global add options to '''clip''', otherwise to '''mclip''' if feasible; Chimera1 has octant stuff in '''vop''' subcommands)
+* '''volume''' isosurface smoothing, and maybe an option equivalent to '''sop hideDust''' (is this used for anything other than isosurfaces?)
+* '''save''' PDB, volume data, ''etc.''
 * '''set''' (or other command) global settings: background color gradient, multiple-layer transparency (correctly rendered even for multiple models)
 * '''setattr''' (or other command) attributes: material properties
-* '''save''' PDB, volume data, ''etc.''
 
 Command accoutrements:
-* more built-in specs like '''protein, nucleic acid,''' functional groups, amino acid categories, element symbols, ''etc.''
+* more built-in specs like '''protein, nucleic acid,''' functional groups, amino acid categories, element symbols, atom types, ''etc.'' (the latter two may have been needed for molecular surface and/or H-bond calculations anyway)
 
 == Would be nice ==
 
-Again listed but not necessarily as commands; mainly expanded functionality of existing commands:
-* '''cartoon''' options for cylinders/pipes, planks (or should these be cartoon options within '''style'''?)
+Again listed but not necessarily as commands: 
+* '''nucleotides''' base-slab, sugar-tube, and ladder 
+  - need better defaults than in Chimera1, at least for smart display
+
+Expanded functionality of existing commands:
+* '''cartoon''' options for cylinders/pipes and planks (or should these be '''style''' options for existing cartoons instead? should also integrate with helix axes, ''i.e.'' the pipes=axes could be used in measurements)
+ - I'm thinking cylinders could be a distinct option for helices, but that we don't really need perfectly box-shaped planks if there is an option for well-smoothed strands (like our default B spline strands in Chimera1)
+* '''style''' option for cartoons, '''tube''' (similar to our current rounded licorice)
 * '''surface''' provisions for multiple surfaces on same atoms, including SAS and/or SES
 * 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 ==