Changes between Version 6 and Version 7 of SurfaceCategories

Timestamp:

May 9, 2015, 3:49:40 PM (10 years ago)

Author:

Elaine Meng

Comment:

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SurfaceCategories

@@ -166 +166 @@
 == Custom surface categories or logical equivalent ==
 
-Even thornier is how to get surfaces enclosing sets of atoms other than the default categories. I don't have a strong opinion on what would be best, but two alternatives come to mind:
+Even thornier is how to get surfaces enclosing sets of atoms other than the default categories. Two alternatives come to mind, of which I favor the second:
 
  - As in Chimera1, keeping surface categories mutually exclusive and allowing the user to move atoms into their own custom categories; then it is unambiguous what would happen after later uses of Actions/Surface or the surface command. Conceptual example (I'm not suggesting these should be the exact commands):
@@ -176 +176 @@
  One disadvantage is that it may be surprising that the default categories get emptied out when new categories are defined, and that it's hard to restore the default categories without closing and reopening the structure.
 
- - Allowing direct specification of the set of atoms to enclose (treat as a category, but without changing the existing categories) in the surface command or !Actions/Surface invocation; however, this would require either showing that whole surface or somehow specifying two sets of atoms, one to define the category and one for which to show the surface patch. Conceptual example:
+ - Probably the better approach, allowing direct specification of the set of atoms to enclose (treat as a category, but without changing the existing categories) in the surface command or !Actions/Surface invocation; however, this would require either showing that whole surface or somehow specifying two sets of atoms, one to define the category and one for which to show the surface patch. Conceptual example:
   - '''surface enclose protein'''
      * ...to surface whole protein in one lump, where “enclose” is a keyword and the atomspec which would have been before it (see [http://www.cgl.ucsf.edu/home/meng/chi2/command-structure.html Chimera2 command structure writeup]) is blank (another complication: above I said '''surface''' with blank atomspec should surface all atoms in categories “main*” ... although that would work OK in this particular example, perhaps it should be overriden by the '''enclose''' keyword to mean all the atoms in the '''enclose''' set, or equivalently, all atoms, period)