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From: Robert H. <ha...@st...> - 2011-06-08 13:41:47
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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 |