Changes between Initial Version and Version 1 of BfactorClip

Timestamp:

Sep 9, 2020, 5:24:01 PM (6 years ago)

Author:

meng

Comment:

--

BfactorClip

@@ +1 @@
+= Color a Sliced Surface by B-factor =
+
+Here is how to color a molecular surface by atomic B-factor,
+including the planar cap where the surface is sliced by a clipping plane.
+
+The following script clips everything, then turns off clipping
+for the atoms so that they can protrude from the sliced surface.
+The atoms of the protein are then colored by B-factor with
+[http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute
+color byattribute]. This automatically colors their patches on the outer
+surface of the protein, but not the sliced surface.
+The atoms themselves are also colored even though they are not displayed,
+and their coloring is then used by
+[http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
+color zone] to color patches in the sliced surface face by the nearest atom.
+
+{{{
+        open 2gbp
+surface
+turn y 70
+clip front 0 position :bgc
+clip model #!1 false
+hide ~ligand target ar
+view ligand :<8 clip false
+style ligand ball
+color C white targ a
+graphics bgColor white
+graphics silhouette true
+color byattribute bfactor protein palette blue:red:yellow:white
+wait 1
+color zone #1.2.1 near protein distance 3 sharp t update t
+}}}
+
+The [http://rbvi.ucsf.edu/chimerax/docs/user/commands/wait.html
+wait 1] is needed only in the context of a command file,
+to force drawing the graphics to create the surface cap before it is colored.
+
+The 'update' option of
+[http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
+color zone] allows subsequently adjusting the clipping plane position
+without having to redo the coloring.
+
+[[Image(bfactorclip.png)]]
+
+Elaine Meng, September 9, 2020
+}
+}