= 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.

[[Image(bfactorclip.png)]]

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 face of the surface.
The protein atoms themselves are also colored by B-factor 
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 the surface cap model (the sliced face) by 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 true' option of
[http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone color zone]
allows subsequently adjusting the clipping plane position
(''e.g.'', with the mouse) without having to redo the coloring.

Elaine Meng, September 9, 2020