Changes between Version 7 and Version 8 of SurfaceCategories

Timestamp:

May 9, 2015, 3:58:01 PM (10 years ago)

Author:

Elaine Meng

Comment:

--

SurfaceCategories

@@ -138 +138 @@
 
   
-== Default surface categories ==
+== Default surface categories (Elaine) ==
+
+These thoughts on handling default and nondefault categories (or whatever you want to call them, sets of atoms enclosed in surfaces) were originally in a [http://www.cgl.ucsf.edu/home/meng/chi2/surfcats.html web page].
 
 Maybe we could use the same default surfcats as in Chimera1, with the modification: splitting main by chain ID. Not sure what the resulting sub-main category names should be, possibly just a concatenation of “main” and the chain ID. 
 
-ECM added 30 Apr 2015: Another modification to consider would be excluding covalently attached ligands from main, especially glycosylations, unless they already have their own separate chain IDs.  If they weren't added to ligand, we would have to come up with some additional name.  Another idea for the names of the main* categories is the type of molecule concatenated with chain ID, something like protA, protB, nucC but still all being shown when surface is used without a specification or selection.
+Another idea for the names of the main* categories is the type of molecule concatenated with chain ID, something like protA, protB, nucC but still all being shown when surface is used without a specification or selection.
 
 Chimera1 default surface categories are mutually exclusive (see [http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats membership rules]):
@@ -164 +166 @@
 In the second example above, one might try '''surface /a''' but that would also surface '''ligand''' ''etc''. with chain ID A, although they would not be in the same category (surface enclosure) as the protein part. This is regardless of whether main is split; it happens in Chimera1 now. It seems like the purpose of the '''solvent''' and '''ions''' categories is to exclude them from any surfaces rather than to surface them, because they are usually monatomic residues. If that remains true, only chain A ligands will be picked up by the simpler command, sometimes even intentionally, so it's not a big problem.
 
-== Custom surface categories or logical equivalent ==
+== Custom surface categories or logical equivalent (Elaine) ==
 
 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:
@@ -176 +178 @@
  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.
 
- - 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:
+ - Probably the better approach is 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)