Otis,
1) It works like a charm, at least with 2-butanol. I understand what
> each line in your script is "saying," but I never could have come up
> with this on my own!
>
>
excellent!
> 2) The find axis component of the script will be of general use to me.
> I've been agonizing over drawing initial structures to align with the
> molecular xyz axis to pre wire structures for Jmol animation scripts.
> It seems that there is no need for this. I need to take a closer look
> at the Jmol math features. I'm embarrassed to admit that I did not
> know that the vector math in your script was a Jmol option.
>
>
If you are having the need to orient structures, try looking into the
quaternion function. It is VERY powerful. Say, for example, you want to
orient a structure so that the atom 3 is at the origin, atom 1 is along x,
and atom 2 is along y. It's as simple as this:
q = quaternion({atomno=1}, {atomno=2}, {atomno=3})
reset;rotate quaternion @{!q}
What we are doing here is to define a frame of reference as a quaternion (a
set of four numbers). The frame is based on a center at atom 1, x axis in
the direction from 1 to 2, and y axis in the plane 1-2-3. The quaternion
describes the rotation necessary to take the default XYZ frame and rotate it
to this frame. The @{!q} notation specifies that we want to rotate the model
by the reverse of this rotation, thus setting the orientation to that
particular frame.
If you don't want to reset the zoom, you can reset the rotation only with:
rotate quatenion @{ !quaternion(script("show rotation")) }
Because the show rotation command returns a quaternion, and negating that
gets you back to the original orientation, like reset, but without the
centering or zoom.
So, together that is:
q = quaternion({atomno=1}, {atomno=2}, {atomno=3})
q0 = quaternion(script("show rotation"))
rotate quaternion @{(!q) / q0}
Here
a) DIVIDE is the same as NOT
b) operation order is from right to left, like matrix multiplication.
c) we need to group the !q in parentheses, because usually NOT is carried
out after * and /, not before.
This reads: "undo the orientation back to the standard view, then undo the
atom-frame rotation.
Probably more than you wanted to know.....
Bob
> 3) I've casually followed the user group for many years, but I only
> recently started asking group questions related to the rebirth of an
> old Jmol project. I don't know the protocol for requests or key words,
> can you point me?
>
> Otis
>
> On Tue, Feb 2, 2010 at 12:38 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> > Otis,
> >
> > It would be good to implement that. Feature request! Suggest a keyword
> > option that would describe this.
> >
> > There is a scripting way to do this. You find the axis perpendicular to
> the
> > two groups, determine the angle required, and rotate one CW while the
> other
> > CCW.
> >
> > Given center {C} and two attached carbons, {Ca} and {Cb}, then:
> >
> > v1 = {Ca}.xyz - {C}.xyz
> > v2 = {Cb}.xyz - {C}.xyz
> > theAxis = cross(v1, v2)
> > theAngle = angle(v1, {0 0 0}, v2)
> >
> > the two groups are found using select within(BRANCH,....)
> > Then you do rotateSelected:
> >
> > select within(BRANCH, {C}, {Ca})
> > rotateSelected MOLECULAR {C} @theAxis @theAngle
> > select within(BRANCH, {C}, {Cb})
> > rotateSelected MOLECULAR {C} @theAxis @{-theAngle}
> >
> > Should do the trick.
> >
> >
> > Bob
> > On Tue, Feb 2, 2010 at 10:36 AM, Otis Rothenberger <o...@chemagic.com>
> > wrote:
> >>
> >> Hello-
> >>
> >> I'm trying to invert the configuration of a single carbon atom. The
> >> symmetry operation of invertSelected inverts the configuration of
> >> target atom attached carbon atoms as well as the target. I tried
> >> selecting only the four target atom attached carbon atoms and then
> >> cleaning up with a minimize. Interesting visual, but again neighboring
> >> atom configuration is inverted after minimization.
> >>
> >> Three questions:
> >>
> >> 1) Am I missing another invertSelected possibility?
> >> 2) Alternatively, is there a general scripting approach to simply swap
> >> two groups attached to the target atom?
> >> 3) Is there an alternative scripting path to my objective?
> >>
> >> Otis
> >>
> >> --
> >> Otis Rothenberger
> >> http://chemagic.org
> >>
> >>
> >>
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> >
> >
> >
> > --
> > Robert M. Hanson
> > Professor of Chemistry
> > St. Olaf College
> > 1520 St. Olaf Ave.
> > Northfield, MN 55057
> > http://www.stolaf.edu/people/hansonr
> > phone: 507-786-3107
> >
> >
> > 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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> >
> >
>
>
>
> --
> Otis Rothenberger
> http://chemagic.org
>
>
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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