Changes between Version 5 and Version 6 of SurfaceCategories

Timestamp:

May 8, 2015, 5:26:14 PM (10 years ago)

Author:

Tom Goddard

Comment:

--

SurfaceCategories

@@ -1 +1 @@
 = Chimera2 surface category thoughts =
 
-== Examples for proposed surface command ==
+== New proposed surface command ==
+
+I think this new syntax is clearer than what I proposed before (TomG).  The first argument is what atoms to use in computing surfaces, and optional keywords handle the rarer uses such as showing a patch of a surface.
+
+To show surfaces for each chain excluding ligands, ions, solvent
+
+  surface #1
+
+To make one surface enclosing all chains excluding ligands, ions, solvent
+
+  surface #1 perChain false
+
+To show just the surface patch of chain surfaces near a ligand
+
+  surface #1 show ligand za<5
+
+I think the above 3 examples are the most common uses.  Now for some exotic cases.
+
+To surface the chains with each chain surface also enclosing the ligands (in this example ligand is an atom spec)
+
+  surface #1 include ligand
+
+To surface just the ligands, one ligand surface per chain.  Here we make an exception
+to the rule that ligands, ions and solvent are excluded -- if only ligands, ions and solvent
+are specified.  This is a convenience.
+
+  surface ligand
+
+To surface several models, one surface per model. Even if per-chain is false it is still per-model.
+
+  surface #1,2,3 perChain false
+
+To put one surface around 3 models
+
+  surface #1,2,3 perModel false
+
+An alternative to the perChain and perModel options would be to have a split option "split chains|models|none".
+
+
+== Earlier proposed surface command ==
 
 Here is a suggestion for how the Chimera 2 surface command could work (TomG).