Takes some getting used to. Basically:
1) You can define little local xyz frames based on any three atoms.
2) You can use "differences" of quaternions -- q1/q2 -- to determine
relative orientation.
3) You can use quaternions in rotation commands in Jmol.
I think the best demo of this is http://chemapps.stolaf.edu/klotho/
Here we have a database that has a wonderful selection of models. But when
you scan through them, they (originally) are in odd orientations. I use
quaternions on the chains to determine what their orientation is and then
reset the orientation to that as they are delivered to the user.
Works like a charm! Take a look at the source of that page. The script looks
like this:
if(what.indexOf("pyranose") >= 0 || what.indexOf("furanose") >= 0 ||
what.indexOf("osamine") >= 0) {
resetScript += '\
anomericC = {_C and connected(2, _O) and connected(4)};\
if (anomericC.size > 0);\
furanose = substructure(\\"[C]1[C][C][C][O]1\\")[1][5];\
pyranose = substructure(\\"[C]1[C][C][C][C][O]1\\")[1][6];\
anomericC = anomericC[1];\
ringO = within(\\"branch\\",anomericC,{_C and
connected(anomericC)})
and {_O} and {connected(anomericC)};\
if (ringO.size == 0);\
ringO = within(\\"branch\\",anomericC,{_C and
connected(anomericC)}[2]) and {_O} and {connected(anomericC)};\
endif;\
anomericO = {_O} and connected(anomericC) and not ringO;\
ringC = within(\\"branch\\",anomericC,{ringO}) and {_C} and
{connected(anomericC)};\
rotate quaternion @{!quaternion(anomericC,ringC,ringO)};\
rotate y 180;rotate x -60;rotate y 20;rotate x 20;rotate y 30;\
if(furanose.size>0 and pyranose.size==0);\
rotate z 20;\
endif;\
center {anomericC};\
set rotationradius 8;\
endif;\
Cool, huh?
:)
Bob
On Wed, Feb 3, 2010 at 12:58 PM, Thomas Stout <thomasjst...@gmail.com>wrote:
> 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
>>> >>
>>> >>
>>> >>
>>> ------------------------------------------------------------------------------
>>> >> The Planet: dedicated and managed hosting, cloud storage, colocation
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>>> >> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>> >
>>> >
>>> >
>>> > --
>>> > 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
>>> >
>>> >
>>> ------------------------------------------------------------------------------
>>> > The Planet: dedicated and managed hosting, cloud storage, colocation
>>> > Stay online with enterprise data centers and the best network in the
>>> > business
>>> > Choose flexible plans and management services without long-term
>>> contracts
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>>> away.
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>>> >
>>> > _______________________________________________
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>>> > https://lists.sourceforge.net/lists/listinfo/jmol-users
>>> >
>>> >
>>>
>>>
>>>
>>> --
>>> Otis Rothenberger
>>> http://chemagic.org
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> The Planet: dedicated and managed hosting, cloud storage, colocation
>>> Stay online with enterprise data centers and the best network in the
>>> business
>>> Choose flexible plans and management services without long-term contracts
>>> Personal 24x7 support from experience hosting pros just a phone call
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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
>>
>>
>> ------------------------------------------------------------------------------
>> The Planet: dedicated and managed hosting, cloud storage, colocation
>> Stay online with enterprise data centers and the best network in the
>> business
>> Choose flexible plans and management services without long-term contracts
>> Personal 24x7 support from experience hosting pros just a phone call away.
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>>
>>
>
>
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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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