Miguel wrote:
I've done a lot with 3D-geometry algorithms. (Nothing really fancy, but...)
As long as Jmol knows internally the coordinates and position for every element, it should be possible for Jmol, by receiving the info on "TYR 97, Chain A, Model 1", to rotate the model if needed and to locate, in the center of the applet, the residue pointing to the user.
Is there something like this available?
Not currently
If not, can you add this command to Jmol?
That sounds like a good idea.
I have not thought of exactly this, but was thinking of a similar/related command called 'moveTo' that would move to a specific position, independent of where the molecule was sitting. Your idea is to extend this by allowing the position to be an atom/set of atoms.
I cannot do this without some help from someone who has a strong mathematics background. I believe that calculating this involves computing an eigenvector to determine the axis of rotation, then calculating the degrees of rotation. It is essentially a great-circle-route calculation. Maybe there is another way to do it, but I really don't know.
So, if someone can help me, I will be glad to do it.
I'm volunteering, but I need a very specific goal. Exactly what is being asked?
Are we trying to do smooth animation or a sudden jump? Does the current user-influenced rotation status need to be a starting point? (Miguel, have you ever thought about having a "phantom axis set, 4 points" rotating with the molecule just for orientation-knowledge purposes?
Bob
Something like this can place the needed residue in the center and zoom on it: rotateTo 97 zoom 200
understood.
Is there something like "blink 5" to have a residue to glow 5 times to call the user's attention?
experiment with 'set display selected' and see what that does. It will not blink, but you should be able to put in few 'delay' commands to achieve the effect that you want.
Miguel
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