Re: [Jmol-users] a treat for you -- Jmol in motion

[Richard S. <ric...@nt...>]

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" <ha...@st...>
To: <jmo...@li...>
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
>
>
>
>
>
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