It's fairly costly, but for small systems it might not be too bad. You can
certainly test this yourself -- just write a function that changes frames
and does the recalculation rather than just doing the animation. Or set up
an animFrameChange callback that includes "autobond"
On Mon, Oct 20, 2008 at 2:45 AM, Angel Herraez <[EMAIL PROTECTED]> wrote:
> Hi
>
> If I have understood it correctly, and my testing suggests so,
> loading several models with the TRAJECTORY keyword makes a single set
> of atoms and bonds, where only coordinates change along frames.
> Therefore, bonding is not recalculated when playing the animation.
> However, I read that cartoons are recalculated and redrawn.
>
> I understand that all this is done so to save memory and to speed up
> things -like in rendering molecular dynamics-.
> My question is, how costly would it be to recalculate bonding at each
> step of the trajectory? This would be helpful e.g. in animating MD
> trajectories with reaction mechanisms, where some bonds are broken
> and others formed. The calculation would mean to draw or not the
> bonds according to atom distance and Jmol default autobonding
> algorithm.
> Such recalculation could be optional, nondefault, and if needed could
> be restricted to a user-specified set of atoms.
>
>
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