Re: [Jmol-users] How to align a molecule with the axis?

[Marco Zimmer-De I. <mar...@gm...>]

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 <ha...@st...> 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 <
> mar...@gm...> 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 <ha...@st...>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 <
>>> mar...@gm...> 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
>>>>
>>>>
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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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>>
>>
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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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>