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
>>
>>
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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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