Thank you for that detailed explanation of quaternions, Bob! This is the
first time I've actually been able to picture how to utilize them in a
general way..... (guess I just needed a different explanation)
-Tom
On Wed, Feb 3, 2010 at 7:09 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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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