Changes between Version 64 and Version 65 of Needed Command Functionality

Timestamp:

May 18, 2015, 10:56:33 AM (10 years ago)

Author:

Elaine Meng

Comment:

--

Needed Command Functionality

@@ -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)
+* built-in specs for element and/or atom type, if already needed for setting radii for molecular surface calculation anyway
 * basic hierarchical atomspecs (see [http://www.cgl.ucsf.edu/home/meng/chi2/frameatom_spec2.html Chimera2 atomspec writeup])
 
@@ -58 +59 @@
 * '''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
+* '''delete'''
 
 Expanded functionality of existing commands:
 * '''open''' (including fetch) cellPACK, which would elicit interface for exploring hierarchy
 * '''select''' all, clear, invert
+* '''set''' and '''setattr''' as mentioned in the previous section
 
 Command accoutrements:
@@ -74 +77 @@
 * '''findhbond'''
 * '''rangecolor''' or equivalent for color-by-attribute
+  - then '''defattr''' would be useful
 * '''scolor''' or equivalent for color-by-scalar (radial, volume value, ''etc.'') 
   - logical to merge '''rangecolor''' and '''scolor''', maybe also '''rainbow''', but what's a good name?
-  - color-by-scalar might only apply to surfaces and atoms
-* '''sop hideDust''' or equivalent
+  - color-by-scalar might only apply to surfaces and atoms, unless we want cartoons to show residue values derived from the substituent atomic values
 * '''define''' geometric objects based on atomic coordinates: axes, planes, centroids, ellipsoids
 * '''shape''' or other way of defining geometric objects arbitrarily
@@ -86 +89 @@
 * '''2dlabels'''
 * '''colorkey'''
-* '''save''' PDB, volume data, ''etc.''
+* '''sop hideDust''' or equivalent (I suggest below it might be a '''volume''' option)
 
 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)
-* '''set''' (or other command) global settings: background color gradient, multiple-layer transparency
+* '''volume''' isosurface smoothing, maybe '''sop hideDust''' equivalent (is this used for anything other than isosurfaces?)
+* '''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: