Title of Your Poster and Project - St. Olaf College

Title of Your Poster and Project - St. Olaf College

The Jmol Voxel (VXL) File Format:
Efficient Delivery of Isosurfaces Over the Web
Robert M. Hanson
Department of Chemistry
St. Olaf College, Northfield, MN

The purpose of the Jmol voxel (JVXL) file format is to provide a mechanism for the efficient delivery of molecular surface
data (orbitals, electron density plots, electrostatic potential maps, solvent surfaces, etc.) from a web server to a client page in a
compact manner. The format was designed to be used specifically with the open-source Jmol molecular viewing and analysis
applet (http://jmol.sourceforge.net), but the format has general utility anywhere the Marching Cubes algorithm is used for
isosurface construction. Compared to data formats such as Gaussian CUBE files, which contain a three-dimensional matrix of
data, the derived JVXL files are 400-1000 times smaller. Jmol can read and write the JVXL file format and is currently the only
application that can be used to create JVXL files.
Note that the resultant client model is fully manipulable and scalable in 3D, not just an image.
Cavities in 3dfr.pdb rendered using Jmol;
file sizes 27K (left), and 37K (right).

Reference URL: http://chemapps.stolaf.edu/jmol

The Method
The Problem
Raw surface data files (CUBE, APBS, etc.) are generally 1-10 Mb.

A map of the electrostatic potential of 1dry.pdb
onto the van der Waals-radius surface. (65K)

The Marching Cubes algorithm is run as for any isosurface, based on a grid
of scalar values and a given cutoff value. The critical edges are identified.
We simply count the number of points alternately outside and inside the
surface.

Sample File
Header Section
grid definition

Transfer of large files over the Web results in unacceptable delays
in page rendering.

optional atomic data

Molecular visualization often requires the display of surface data.

comments

JVXL encoding defs
character counts
color mapping parameters

The Idea
Molecular surfaces are not really 3D objects. Rather,
they are 2D objects embedded in three dimensions.
Most of the data in a CUBE file is unnecessary for the
display of any particular surface.
Only the data necessary to specify a particular surface
needs to be transferred.

The Solution
Consider the underlying 3D grid containing the surface of interest.

Edge Section I
The interpolated surface intersection point is identified as a distance along
the critical edge, expressed as a number between 0 and 90. This number is
encoded as a ASCII digit in the range 35 124, inclusive, with 92
(backslash) recorded as 33 (exclamation point). ASCII 125 } is reserved
for indicating no value, thus allowing for surface fragments.
0.0
.
.
.
.
1.0
#$%&()*+,-./0123456789:;<=>[email protected][!]^_`abcdefghijklmnopqrstuvwxyz{|
0 (ASCII 35)
.
.
.
.
89 (ASCII 124)

Note that this format allows for the information to be passed within doublyquoted strings, and with any number of line breaks.
Finally, if the surface point is to be mapped with a value from another grid,
that value is base90-encoded in the same way as the intersection point, with
the option to encode the remainder as a second base90 value, thus allowing
for a precision of 1 part in 8100 if desired. (This was found important for
planar surfaces.)

identifies critical edges
Edge Section II
identifies precise location
of intersection of surface
and grid along each critical
edge, base90-encoded
Color Map Section
identifies the color to assign
each grid intersection point,
base90-encoded

JVXL solvent-excluded surface
range (-3.6571667, -3.3279688, -1.95) to (3.6571667, 3.3279688, 1.95)
-12 -6.9110436 -6.28895 -3.684966
24 0.6581947 0.0 0.0
22 0.0 0.6619947 0.0
14 0.0 0.0 0.6699939
1 1.0 4.643372 0.0 0.0
6 6.0 2.616899 0.0 0.0
6 6.0 -2.616899 -0.0 0.0
6 6.0 1.3084495 2.2663012 0.0
6 6.0 1.3084495 -2.2663012 0.0
6 6.0 -1.3084495 -2.2663012 0.0
6 6.0 -1.3084495 2.2663012 0.0
1 1.0 2.3216863 4.0212784 0.0
1 1.0 2.3216863 -4.0212784 0.0
1 1.0 -2.3216863 -4.0212784 0.0
1 1.0 -2.3216863 4.0212784 0.0
1 1.0 -4.643372 -0.0 0.0
-1 35 90 35 90 Jmol voxel format version 0.9f
#
# load C6H6.smol;isosurface delete resolution 3 solvent map mep
0.0 1347 1272 1272 -0.09553222 0.036691315 -0.09553222 0.036691315
424 4 10 4 10 4 10 4 248 4 9 6 8 6 8 6 8 6 9 4 207 2 10 6 8 6 7 8 6 8 6 8 6 8 7 6 8 6 10 2 138 2 11 4 9 6 8 6 7 8 6 8 5 10 4 10 4 10 4 10 5 8 6 8 7 6 8 6 9 4
11 2 82 2 11 4 9 6 7 8 6 8 6 8 5 10 4 10 4 10 4 10 4 10 4 10 5 8 6 8 6 8 7 6 9 4 11 2 67 4 9 6 7 8 6 8 5 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 5 8
6 8 7 6 9 4 66 4 9 6 7 8 5 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 5 8 7 6 9 4 66 4 8 8 5 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10
4 10 4 10 4 10 4 10 5 8 8 4 66 4 8 8 5 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 5 8 8 4 66 4 9 6 7 8 5 10 4 10 4 10 4 10 4 10 4
10 4 10 4 10 4 10 4 10 4 10 4 10 5 8 7 6 9 4 66 4 9 6 7 8 5 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 5 8 7 6 9 4 66 4 8 8 5 10 4 10 4 10 4
10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 5 8 8 4 66 4 8 8 5 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 5 8 8 4 66 4 9
6 7 8 5 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 5 8 7 6 9 4 66 4 9 6 7 8 6 8 5 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 4 10 5 8 6 8 7 6
9 4 67 2 11 4 9 6 7 8 6 8 6 8 5 10 4 10 4 10 4 10 4 10 4 10 5 8 6 8 6 8 7 6 9 4 11 2 82 2 11 4 9 6 8 6 7 8 6 8 5 10 4 10 4 10 4 10 5 8 6 8 7 6 8 6 9 4 11 2
138 2 10 6 8 6 7 8 6 8 6 8 6 8 7 6 8 6 10 2 207 4 9 6 8 6 8 6 8 6 9 4 248 4 10 4 10 4 10 4 1070
[email protected][email protected]^11^JFGhnhnJGYXXEXEG:kke:kkeXEEGGFGnnGGYU77U-i'-'6$|#dSjjdS$##$hh{{PP{PO:gge:ggePPPO$
$hh${|#SjjS##{;i'';6{rr4!-4-C=n+GG=+1%z$K^^K%$%KEmmET5t-5-+;{{dIm=I=2Z[[EZ[[Em==2V;{{Vdt--+jKEmmEjTz$K^^K$%[email protected]/[email protected]^^!1nUlKUK3IV7h7hIVlKK3J1JnC^^!f999ZMIIZR5.ff5q)/EE)p__MAtllMt^!Pm!
mOF]MFMB&ytbOtO=XeeGOP7h'x'x7hOPXeeGbOO=+&+y]MMBYPmmYOCAttC^R33R!.yy!qr(rww2wmc[vcvD?`5j:e4k&y&y4k:e5j?
`[vvD<2*>(IV.q${+tB]SLSLB]+t$
{.qIVw>>(ujssu5l0A0^leSSeM6kkMi3jqq35)x)'IV.q%z+t8g6i6i8g+t%z.qIVx'vjv5l.6.ilR44R!.yy!q6r(rw6ew2wmec[cD?`5j:e4k&y&y4k:e5j?
`[D

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