This is a call for those interested in molecular surfaces.
I've had some great success lately redesigning the way Jmol creates
solvent-excluded surfaces, and I need some help. What I'm interested in
doing is comparing Jmol's surface creation with both PyMOL and the MSMS
program (http://mgltools.scripps.edu/packages/MSMS/). I think this might be
significant enough to consider publication. It is not MSMS, but it
reproduces the result of MSMS VERY closely and perhaps better than MSMS
itself. I have no idea how PyMOL generates these surfaces -- it may just be
a straight implementation of MSMS, but I don't know. (I think not, because I
see there's an MSMS plug-in for PyMOL. In the course of transferring to a
new laptop, I haven't gotten PyMOL set up, so I haven't checked that out.)
I'm interested in testing cases with cavities and various other oddities,
comparing Jmol, PyMOL, and MSMS.
Nico has released Jmol 12.1.27, which introduces this new way of creating
surfaces, and tweaks today I have made make some subtle changes -- see
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
Here's a sample output that I created:
http://chemapps.stolaf.edu/jmol/docs/misc/msmsTest.png
In this image, the green is Jmol. The orange is MSMS triangulation. The
reason the image is so patchy is that the surfaces are almost identical. The
tent-like tripods are Jmol's calculated analytical solution to the problem.
The tripods are places where the solvent probe sits on three atoms. Green
means the solvent probe is well above the plane connecting the three atoms;
red means the solvent probe intersects that plane. The white/green or
white/red boundaries are at the solvent probe radius.
The surfaces are almost identical. Interestingly, though, MSMS and Jmol
generate the surfaces in two totally different ways -- MSMS creates a
"reduced surface" and uses that to generate a network of triangles
representing the solvent-excluded surface directly from the analytical
solution, stitching them together as needed; Jmol never creates a reduced
surface and never has to do any "stitching." Instead, Jmol identifies all
edges and faces that are required for the generation of the surface (like
MSMS), then generates a grid of point-values representing distances from the
surface, and then uses the Marching Cube algorithm to generate the surface
from that. The starting point is the same, but Jmol's process is quite
different. Also, Jmol's measure of the surface area, 2269 A^2, is closer to
the analytical solution reported by MSMS, 2258 A^2, than the MSMS
triangulation (2214 A^2). Even if I increase the triangulation for MSMS more
than two fold, it still doesn't get as close to the analytical result as
Jmol's. Thus, I think we really have something here. Besides, this is open
source....
If you are interested in participating in this test and in writing a paper
about it, let me know. Just for future reference, I'm adding some more
information below, before I forget what I did. The command sequence for
comparison is given below.
Bob
## creating the MSMS surface:
load =1crn
script "http://chemapps.stolaf.edu/jmol/docs/examples-12/drawMsMs.spt";
set defaultVDW babel
load xxxx.pdb
writeXyzrn("1crn")
[ then used the following command:
msms -probe_radius 1.5 -density 3 -if 1crn.xyzrn -of 1crn
to create the MSMS surface -- density 5 is probably more appropriate for
comparison.]
isosurface s1 color orange 1crn.vert
# creating the Jmol surface, with the tripods:
set logfile "msms.log" # logging ON generates a file of draw commands for
the tripods
log "$CLEAR$"
isosurface s2 color green solvent 1.5 FULL
log ""
script JmolLog_msms.log
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Learn how Oracle Real Application Clusters (RAC) One Node allows customers
to consolidate database storage, standardize their database environment, and,
should the need arise, upgrade to a full multi-node Oracle RAC database
without downtime or disruption
http://p.sf.net/sfu/oracle-sfdevnl
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
