Couldn't help noticing a matrimonial theme on following the DNA link! Is this intentional?
Keep up the good work! Best wishes Richard Steane Near Guildford, Surrey, UK Website http://www.BioTopics.co.uk dedicated to teaching and learning Biology ----- Original Message ----- From: "Bob Hanson" <[EMAIL PROTECTED]> To: <[email protected]> Sent: Wednesday, February 28, 2007 8:57 AM Subject: [Jmol-users] a treat for you -- Jmol in motion > Hot off the press -- > > Q: What do you get when you combine the following? > > wide-ranging variable capability, including arrayed variables > program flow control with if/else/endif and message/loop > relative motion > > > Take a look at http://www.stolaf.edu/people/hansonr/molecules.htm > in particular the link "Water Liquid" followed by "Jmol 11.2 motion ON" > > This is not a movie. This is not a set of frames. It's just a file full > of water molecules. > > Then look at the script that drives the animation: > > http://www.stolaf.edu/people/hansonr/water.spt > > This script runs through the molecules, setting them moving in > independent directions. It tracks what direction they are going and how > many atoms are within 1.6 angstroms of a given molecule. When nearby > atoms are found, the program reverses a molecule's direction, but if a > molecule wander too far afield, we can spot that and turn it around > again. The code that controls this neighbor-sensing and reversal is just > a few lines long: > > tooclose = not {mol_set} and within(1.6, {mol_set}) > if (tooclose > 0) > set @vm = mxyz - {tooclose_set}.xyz > else > if (centerpt.distance(mxyz) > maxradius) > set @vm = {0 0 0} - @vm > endif > endif > > motion = @vm / @vm * rate > select {mol_set} > translateSelected @motion > > > Pretty straightforward! > > The setup is interesting as well: > > centerpt = {*}.xyz > nMolecules = {*}[{*}].molecule > > message _start # this is the loop start > > m = m + 1 > if (m > nMolecules) > m = 1 > endif > > mol = {molecule=m} > mxyz = {mol_set}.xyz > vm = "v"+m # this is the "array" - v1, v2, v3, etc. > set @vm mxyz # this sets the appropriate variable, v1, v2, etc. > > > > > > Fun, eh? > > -Bob > > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
