Changes between Version 3 and Version 4 of SurfaceCategories

Timestamp:

May 7, 2015, 5:22:30 PM (10 years ago)

Author:

Tom Goddard

Comment:

--

SurfaceCategories

@@ -5 +5 @@
 Here is a suggestion for how the Chimera 2 surface command could work (TomG).
 The basic idea is to surface by chain (no ligands, solvent, ions), but allow surfacing whole proteins as another option, and allow surfacing any atoms as a rare case.  The rule to ignore ligands, solvent and ions unless only those are specified is tricky but I think necessary to handle the common case in a simple way.
+
+The Chimera 1 notion of "surface categories" is not used, although general purpose atom specifiers "ligand", "main", "solvent" would still be available for use with any command.  The proposed surface command has a built-in capability to do per-chain surfacing and ignores ligands, ions and solvent unless extra options are specified.
+
+Examples follow.
 
 To surface each chain of #1 excluding ligands, solvent, ions:
@@ -13 +17 @@
 
    surface enclose #1
+
+In Chimera 1, the command surface #1 creates one surface enclosing all chains not including ligands, ions, solvent and another surface enclosing all ligands.  With the proposed Chimera 2 surface command this would be done using two commands.  I think it is not so common that the ligand surface is desired.
+
+   surface enclose #1
+   surface enclose ligand
 
 To surface just chain A of #1 which has chains A,B,C:
@@ -26 +35 @@
    surface #1/A:10-20 enclose #1
 
-To surface just the ligands.  Above I said "surface #1" excludes ligands but "surface ligand" includes them -- if the specifier is empty when ligands, ions and solvent are thrown out but not empty when they are kept, then keep them.
+To surface just the ligands, the ligands of each chain being a separate surface use the following command.  Above I said "surface #1" excludes ligands but "surface ligand" includes them -- if the specifier is empty when ligands, ions and solvent are thrown out then keep them.
 
    surface ligand