I have some real goodies in 11.9.19 for you. Read these independently, and
then see how they all come together in the end.
isosurface WITHIN
# new feature: isosurface WITHIN 2.0 {atom expression}
# gives true calculation of surface within that distance
# of ANY atom in the set, not just the center
boundbox $isosurfaceID
allows setting the boundbox to the isosurface boundaries
center $isosurfaceID
allows centering on an isosurface
boundbox SCALE x.xx
# boundbox scale 0.5 # scales the current boundbox
# boundbox scale 1.1 {*} # scales the boundbox to 10% larger than usual
# boundbox scale 1.1 CORNERS {first} {second}
# boundbox scale 1.1 {center} {cornerVector}
# boundbox scale 1.1 $isosurface1
XPLOR MAP electron density reader
CCP4 MAP electron density reader
these surface data readers are now available and are not limited by the size
of the grid. 200x200x200 is no problem.
OK, all together now:
load =1w2i
boundbox scale 1.1 {strucno=2} on
isosurface color yellow within 2.3 {strucno=2} "xplor.map" mesh nofill
frontonly
zoomto {strucno=2} 0
The result is shown at
http://chemapps.stolaf.edu/jmol/docs/examples-11/data/1w2i_xplor.png
Oh, and while the XPLOR file is 65 MB, the JVXL rendition of the entire unit
cell is just 200K -- a compression factor of about 300:1. The JVXL rendition
of just this part of the surface is only 36K -- almost a factor of 2000
fewer bytes
Now we're talkin'!
Bob
--
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
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