Rolf,
console problem -- yes, I saw that on a Mac last weekend. I'll look into
it. Something about the way the mouse events are being handled in Safari, I
think. Can you try Firefox or Very frustrating!
rotate: sorry, I can't reproduce that, hard as I try.
Rotate BEST
executes this:
q = getQuaternionParameter(i,
viewer.getRotationQuaternion().mul(-1));
And then rotates the model by that quaternion.
Now, the calculation is the same no matter how you have rotated the
structure. That second parameter simply applies the reverse of the current
quaternion rotation at the and adds it to the overall rotation. Provided
the same set of atoms is chosen, it must give the same rotation, because
the first thing it does is return the model to the "reset" orientation.
I don't doubt that you are getting different rotations. I just don't think
it's by those directions.
It's very important that you not issue
rotate SELECTED best
because that will change the atom coordinates, and then you could in
principle get a different rotation the second time. But obviously you are
not doing that.
Bob
On Tue, Aug 20, 2013 at 10:46 AM, Rolf Huehne <rhue...@fli-leibniz.de>wrote:
> On 08/20/2013 04:20 PM, Robert Hanson wrote:
> > Hmm. Shouldn't work that way. ROTATE BEST initializes with a "restore
> > orientation" (or, at least it effectively does that, because it
> multiplies
> > in the inverse of the current rotation quaternion).
> >
> > What was the exact sequence of commands you used there? As far as I know,
> > the only way it can give a different rotation is
> >
> > a) if you change the set of selected atoms, or
> > b) if you change the atom positions themselves.
> >
> > I could be wrong, but the algorithm must give the same quaternion result
> > every time if it is using the same positions. Don't think I had a fixed
> bug
> > regarding that, but in any case, use
> >
> > http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.20.zip for
> testing,
> > please.
> >
> Unfortunately I have a problem with the Jmol console (see below) so that
> I cannot just paste the exact sequence. But it is more or less
> reproducible, also with Jmol.jar from the ZIP file above. I did for
> example this:
>
> 1) load =108L; select not water
> 2) rotate best [results in first orientation]
> 3) select sheet
> 4) rotate with the mouse
> 5) select not water
> 6) rotate best [results (often) in a different orientation]
>
> Step 4 and 5 might also be inverted.
>
> The problem with the console is really weird. If the mouse gets to the
> yellow frame around it, the console moves away from it (down left or
> right). It is impossible to move the mouse into it.
> After reloading the page it was first normal again. But after dragging
> the console around with the mouse the same weird behaviour was back.
>
> Regards,
> Rolf
>
> --
>
> Rolf Huehne
> Postdoc
>
> Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
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