You'll have to give me a specific example. Flick is using Jmol 11.6 there,
but if you upgrade it to 12.1 using:
http://www.wellesley.edu/Chemistry/Flick/ligandfield.html?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar
then you can see what I am talking about.
Select square planar and dyz
Wait for the orbital to show up. (He's using CUBE files instead of just
generating the atomic orbitals directly, poor guy! :)
Right-click to get a console, then enter this in the console:
M = {0 0 0};A = {0 1 -1}; B={0 1 1};x=90; spin @{quaternion({1 0 0}, x) *
(!quaternion(M, A, B)) * (!quaternion(script("show rotation")))} -1
You can experiment with different values for M, A, B, and X, and I am sure
you will get what you are looking for. Or tell me again what that is you are
looking for.
Bob
On Mon, Oct 18, 2010 at 12:31 PM, Marco Zimmer-De Iuliis <
[email protected]> wrote:
> OK,
>
> I think that is doing something, but not quite.
>
> Here is a website along the lines of what I would like to try to do.
>
> http://www.wellesley.edu/Chemistry/Flick/ligandfield.html
>
> It is a jmol page and if you click on the octahedral filed, then the point
> charges are located such that the align with the axes.
>
> http://www.wellesley.edu/Chemistry/Flick/ligandfield.html
>
> I want to something similar - maybe it is a matter or re-orienting the
> molecular coordinates?
>
> thanks,
> Marco
>
>
> On Mon, Oct 18, 2010 at 12:26 PM, Robert Hanson <[email protected]>wrote:
>
>> Marco, you haven't defined axisRotation then. Don't worry about it. That
>> was just an example.
>>
>> By default, the z axis points toward you; the x axis is horizontal; the y
>> axis is vertical.
>>
>> What are the coordinates of:
>>
>> A) the point you want to be directly between you and the metal atom, which
>> I will call M?
>>
>> B) the point you want to be to the right?
>>
>> Then you would use this:
>>
>> Var q = quaternion(M, A, B)
>> Var qCurrent = quaternion(script("show rotation"))
>> rotate @{(!q) * (!qCurrent)}
>> rotate x 90
>>
>> That says, "Create a quaternion reference frame based on x=M-A and y=M-B.
>> Also get the current rotation frame. Now undo both of these rotations (first
>> the current rotation, then the desired reference frame). At this point, m-A
>> will be pointing to the right, and M-B will be pointing vertically in the
>> plane of the screen. Now rotate M-B to be pointing toward the observer."
>>
>> for example,
>>
>> load SF6.smol
>> var M = {_S}
>> var A = {atomno=2}
>> var B = {atomno=3}
>> Var q = quaternion(M, A, B)
>> Var qCurrent = quaternion(script("show rotation"))
>> rotate @{(!q) * (!qCurrent)}
>> rotate x 90
>>
>> Bob
>>
>>
>>
>> On Mon, Oct 18, 2010 at 10:48 AM, Marco Zimmer-De Iuliis <
>> [email protected]> wrote:
>>
>>> Thanks for your response.
>>>
>>> I tried what you suggested but the last line "rotateSelected molecular
>>> @axisRotation @theta" gives me
>>>
>>> "script ERROR: invalid argument
>>> ----
>>> rotateSelected molecular >> <<"
>>>
>>> I guess I was not very clear in my first e-mail. What I would like is
>>> for the bonds to line up along the coordinate axes when one uses the "axes
>>> on" command. Right now, I have the metal atom at the origin, but the
>>> ligands in the apex positions are pointingsuch that they are +45 degrees in
>>> the xy plane and -90 degrees in the z plane (based on having the z axis
>>> vertical, the x axis pointing out of the screen and the y axis in the plane
>>> of the screen).
>>>
>>> I don't know if that helps.
>>>
>>> Marco
>>>
>>>
>>> On Fri, Oct 15, 2010 at 5:02 PM, Robert Hanson <[email protected]>wrote:
>>>
>>>> # get vector to align with Z:
>>>> Var vectorXY = {atomno=3}.xyz - {atomno=1}.xyz # perhaps
>>>>
>>>> # get cross product for axis of rotation:
>>>> Var axisRotation = cross(vectorXY, {0 0 1})
>>>>
>>>> # get angle of rotation as a dihedral:
>>>> Var theta = angle(vectorXY, {0 0 0}, axisRotation, {0 0 1})
>>>>
>>>> select *
>>>> rotateSelected molecular @axisRotation @theta
>>>>
>>>> Now, this actually changes the coordinate positions. Hard to know what
>>>> you mean by "the axis that is displayed in Jmol" --- That could be the
>>>> molecular axis, the current Z axis for the window, or other things.
>>>>
>>>> Do you just want to "look down a bond"? If so, rather than doing that,
>>>> can you perhaps "look down a bond with a certain atom to the right"? That I
>>>> can show you how to do with quaternions.
>>>>
>>>> Bob
>>>>
>>>> On Fri, Oct 15, 2010 at 12:50 PM, Marco Zimmer-De Iuliis <
>>>> [email protected]> wrote:
>>>>
>>>>> Hello all,
>>>>>
>>>>> I am trying to make an octahedral molecule align with the axis that is
>>>>> displayed in JMol.
>>>>>
>>>>> The central metal atom is at the origin, but I would like to have the
>>>>> metal ligand bonds aligned with the axis.
>>>>>
>>>>> I don't know how to re-set the axis to move it or how to find the
>>>>> coordinates of the atoms.
>>>>>
>>>>> Any help would be greatly appreciated.
>>>>>
>>>>> Cheers all and have a nice weekend.
>>>>>
>>>>> Marco
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Download new Adobe(R) Flash(R) Builder(TM) 4
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>>>>> across multiple browsers and platforms. Download your free trials
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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
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Download new Adobe(R) Flash(R) Builder(TM) 4
>>>> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
>>>> Flex(R) Builder(TM)) enable the development of rich applications that
>>>> run
>>>> across multiple browsers and platforms. Download your free trials today!
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>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Download new Adobe(R) Flash(R) Builder(TM) 4
>>> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
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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
>>
>>
>> ------------------------------------------------------------------------------
>> Download new Adobe(R) Flash(R) Builder(TM) 4
>> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
>> Flex(R) Builder(TM)) enable the development of rich applications that run
>> across multiple browsers and platforms. Download your free trials today!
>> http://p.sf.net/sfu/adobe-dev2dev
>> _______________________________________________
>> Jmol-users mailing list
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>>
>>
>
>
> ------------------------------------------------------------------------------
> Download new Adobe(R) Flash(R) Builder(TM) 4
> The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
> Flex(R) Builder(TM)) enable the development of rich applications that run
> across multiple browsers and platforms. Download your free trials today!
> http://p.sf.net/sfu/adobe-dev2dev
> _______________________________________________
> Jmol-users mailing list
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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
------------------------------------------------------------------------------
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The new Adobe(R) Flex(R) 4 and Flash(R) Builder(TM) 4 (formerly
Flex(R) Builder(TM)) enable the development of rich applications that run
across multiple browsers and platforms. Download your free trials today!
http://p.sf.net/sfu/adobe-dev2dev
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