Changes between Version 1 and Version 2 of SurfaceCategories

Timestamp:

Apr 23, 2015, 5:50:34 PM (11 years ago)

Author:

Tom Goddard

Comment:

--

SurfaceCategories

@@ -1 +1 @@
 = Chimera2 surface category thoughts =
 
+== Examples for proposed surface command ==
+
+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.
+
+To surface each chain of #1 excluding ligands, solvent, ions:
+
+   surface #1
+
+To surface all atoms in one surface use the "enclose" option which automatically excludes ligands, solvent and ions:
+
+   surface enclose #1
+
+To surface just chain A of #1 which has chains A,B,C:
+
+   surface #1/A
+
+To surface chain A but only show residues 10-20:
+
+   surface #1/A:10-20
+
+To surface the whole molecule excluding ligands, solvent, ions, but only show chain A residues 10-20
+
+   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.
+
+   surface ligand
+
+To surface ligands only of molecule #1 when other molecules are open:
+
+  surface #1 & ligand
+
+To surface #1 including main and ligands per chain use "ligands" keyword option:
+
+  surface #1 ligands true
+
+To change which patch is being displayed of an already created surface. In this example the first command creates the chain A surface showing residue 10-20.  The second command modifies the existing surface because it sees that the chain A surface already exists (exact same set of atoms surfaced):
+
+  surface #1/a:10-20
+
+  surface #1/a:30-40
+
+If you want two copies of a surface enclosing the exact same set of atoms
+
+   surface #1 copy true
+
+Now how do you change the two surfaces to show different patches?
+
+   surface #1/a:10-20 using #1.1
+
+   surface #1/a:30-40 using #1.2
+
+What will the model numbers be for surfaces?
+
+   surface #1
+
+produces (the model name is "surfaces")
+
+   #1.1 surfaces
+
+and if #1 has three chains these will be
+
+   #1.1.1 A
+
+   #1.1.2 B
+
+   #1.1.3 C
+
+Probably model panel will not show that third level by default, you would need to expand the line "#1.1 surfaces" to see them.  If you then make another surface
+
+  surface enclose #1
+
+you get another model (with no children since the enclose option produces a single surface)
+
+  #1.2 surface
+
+and the #1.1 surfaces still exist and could be closed if desired with
+
+  close #1.1
+
+If you surface two or more molecules with one surface (rare situation)
+
+   surface enclose #1 | #2
+
+then the resulting surface model will be #3 (or the next available model number) instead of being a child of either model.
+
+  
 == Default surface categories ==