Even better. Just use that code, but put in the specific ligand atom names
or numbers, and it will pop right up into the correct orientation.
If you are trying to actually change the coordinates to new coordinates,
then use
rotate selected
instead of just rotate or spin, and it will actually change the coordinates.
For example:
just rotating:
M = {0 0 0};A = {atomno=2}; B={atomno=7};x=90;
spin @{quaternion({1 0 0}, x) * (!quaternion(M, A, B)) *
(!quaternion(script("show rotation")))} -1
or, if you want to change the coordinates, you don't have to use the "show
rotation" business, but instead in the end need a RESET command to reset the
orientation of the axes.
M = {_Mo};A = {atomno=2}; B={atomno=7};x=90;
rotate selected molecular @{quaternion({1 0 0}, x) * (!quaternion(M, A, B))}
reset
I notice that the molybdenum is not centered. So if you want that at the
origin, do this:
translateselected @{-{_Mo}.xyz}
$ getproperty extractmodel
C:\jmol-dev\workspace\Jmol\bobtest\mo.log
Jmol version 12.1.16_dev 2010-10-12 07:49
EXTRACT: ({0:6})
7 0 0 0 0
0.0 0.0 0.0 Mo
1.3999995 0.0 0.0 Xx
-1.399999 0.0 0.0 Xx
0.0 1.3999996 0.0 Xx
0.0 -1.4 0.0 Xx
0.0 0.0 -1.4 Xx
0.0 0.0 1.4 Xx
However, I suspect you want the first, not the second, because if you change
the coordinates, the MOs are all going to be messed up.
Bob
On Tue, Oct 19, 2010 at 8:28 AM, Marco Zimmer-De Iuliis <[email protected]
> wrote:
> OK.
>
> I see what you are saying - I have played around with the command you
> showed me and I can see how it moves the orbital around in space. But the
> ligands are aligned with the axes, which is not the case with my log file.
>
> I will send you my log file. Its is molybdenum, with 6 dummy atoms arranged
> in an octahedral ligand field.
>
> When you open it, and type in "axes on", then the Metal-ligand bonds don't
> correspond to the coordinate axes that appear when you type in "axes on".
>
> I greatly appreciate your help on this - I am trying hard to figure out
> Jmol on my own but I don't have any background in java programming or html
> coding, so it is a steep learning curve for me.
>
> Cheers,
> Marco
>
>
> On Mon, Oct 18, 2010 at 3:05 PM, Robert Hanson <[email protected]> wrote:
>
>> 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
>>>>>>> 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
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>>>>>>> across multiple browsers and platforms. Download your free trials
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>>>>>>> _______________________________________________
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>>>>>>> [email protected]
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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
>>>>>> [email protected]
>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> 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
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>>>>> Jmol-users mailing list
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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
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>> [email protected]
>>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> [email protected]
>> 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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across multiple browsers and platforms. Download your free trials today!
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