[chimerax-users] color offset and surface type for mapping Electrostatic Potential

[Steve Chou]

Hello everyone,

I tried to map Electrostatic Potential (ESP) onto the molecular surface in
ChimeraX v1.0 and PyMOL v2.1, but I found that the results were very
different in these two programs. Therefore, I wrote to Elaine Meng and Tom
Goddard for help. For your reference, I repost the ideals of our emails
below.

I first calculated the ESP with DelPhi v5.1 (a relatively old version) to
get the .phi file (ESP).

PyMOL commands for displaying ESP on the molecular surface are as follows:
------------------------------------------------
load 1ubq.pdb
bg_color white
remove resn hoh
remove hydrogens
hide line
select  heavy, name c*+o*+s*+n*
show surface
load 1ubq.phi, e_map
ramp_new e_lvl, e_map, [-7, 0, 7]
set surface_color, e_lvl, 1ubq
set light_count, 1
set ambient, 0.5
set reflect, 0.2
------------------------------------------------

ChimeraX commands for displaying ESP on the molecular surface are as
follows:
------------------------------------------------
open 1ubq.pdb
open 1ubq.phi
hide #2
set bg white
surface #1
color electrostatic #1 map #2  palette -7,red:0,white:7,blue
material dull
lighting simple
------------------------------------------------

In PyMOL, the colors (red/blue) are mainly on the residue (E/D, K/R) tips,
while in ChimeraX, the colors are spread. Besides, the surface shapes are
also slightly different in these two programs. See the image (left and
middle panels) for the different colors and shapes.

The color difference is caused by the color offset. The shape difference is
also explained below. I changed the color offset to 0. Now the color looks
similar in these two programs (left and right panels). The color offset
(1.4 A) in ChimeraX gives a better idea of the possible charge interactions
with other molecules.
------------------------------------------------
color electrostatic #1 map #2  palette -7,red:0,white:7,blue offset 0.0
------------------------------------------------

The summary of the explanations from Tom:
------------------------------------------------
One idea I have for why PyMol shows redder tips is because ChimeraX is
showing the potential 1.4 Angstroms away from the surface since that is
about how far away a binding molecule would be. PyMol may be showing the
ESP values exactly on the surface.  You can try using 0 offset instead of
1.4 with the "color electrostatic" command "offset" parameter.
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#map
------------------------------------------------
The summary of the explanations from Elaine:
------------------------------------------------
As Tom mentioned, the rationale for the 1.4 A projection is that Chimera
and ChimeraX show the solvent-excluded surface (SES), as opposed to the
solvent-accessible surface (SAS). The SAS is approximately half a probe
radius outward, and the SAS represents the closest possible approach of
atomic centers of waters or ligands interacting with the protein, so the
result is coloring by what values of the electrostatic potential (ESP) that
such ligands would "see". The diagram in this page shows the relationships
among  SES, SAS, and probe.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>

Possible reasons for difference in Pymol, if the ESP map itself is
identical:
(1) coloring by offset values or not.  It has been my general understanding
that when programs color the SES by ESP, the default approach is to color
by the values one surface-probe radius outward.
(2) shape/location of the surface.  Is it an SES or SAS, or neither?
Pymol surfaces often look more "melty" or smoothed to me than the SES in
Chimera/ChimeraX.
(3) the exact color-mapping, i.e. which colors at which values. Pymol ESP
coloring often uses a duller-looking blue.
------------------------------------------------

All the best,
Steve


-- 
Steve Chou
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