[Jmol-users] Jmol and NCIPLOT

[Robert H. <ha...@st...>]

noncovalent interactions are not viewable in Jmol -- or at least will be,
once the next version is released. Currently only in
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

But here's a teaser: http://www.youtube.com/watch?v=ZM_KFjHRGXQ

Created with this script using Jmol 12.1.49_dev:


load gb-nci.xyz
reset;center {-2.9921532E-5 0.025004983 4.9471855E-6}; rotate z -46.43;
rotate y 84.95; rotate z 62.91;

rotate branch {c5} {C8} 20
for (var i = 0; i < 15; i++) {
  rotate branch {c5} {C8} -10
  isosurface NCI
  refresh
  write @{"c:/temp/nci-test-rotate-" + i + ".png"}
  write @{"c:/temp/nci-test-rotate-" + i + ".jvxl"}
}


Then put together with Windows MovieMaker for the YouTube video, or you can
also just replay it in Jmol using:

load gb-nci.xyz
reset;center {-2.9921532E-5 0.025004983 4.9471855E-6}; rotate z -46.43;
rotate y 84.95; rotate z 62.91;

rotate branch {c5} {C8} 20
for (var i = 0; i < 15; i++) {
  rotate branch {c5} {C8} -10
  isosurface @{"c:/temp/nci-test-rotate-" + i + ".jvxl"}
  refresh
}


-- 
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