# 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
Andreas, I really don't think it's Jmol.
What you need to do (is this a browser?) is to completely close all windows
of your browser, including the download window, transfer the new files into
the directory, and then restart your browser. These aren't standard errors.
They must be problems because
Thanks for the quick update,
now I am getting a different exception. This one has been present also in
older versions of Jmol... (again PDB ID 3CDZ )
Exception in thread "QueueThread1" java.lang.ArrayIndexOutOfBoundsException:
7
at org.jmol.viewer.ColorManager.getColixAtomPalette(Unknown Source)
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 th
On Fri, Oct 15, 2010 at 9:08 AM, Otis Rothenberger wrote:
> Bob,
>
> I realize that random errors are hard to analyze without specific
> circumstances, but I thought that you might have some "likely suspect"
> thoughts on the following two that pop up from time to time:
>
> 1) On an applet load,
Bob,
I realize that random errors are hard to analyze without specific
circumstances, but I thought that you might have some "likely suspect"
thoughts on the following two that pop up from time to time:
1) On an applet load, a Jmol.js for: "if (applet)
applet.script(script);" (line 410 in 12
OK, I've uploaded a rebuilt copy of the binary. Works with that script for
me.
On Fri, Oct 15, 2010 at 8:01 AM, Robert Hanson wrote:
> I must have messed up building that. I'll rebuild it and upload the files
> again.
>
> This should work:
>
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmo
I must have messed up building that. I'll rebuild it and upload the files
again.
This should work:
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12_0.zip
On Thu, Oct 14, 2010 at 6:49 PM, Andreas Prlic wrote:
> Hi,
>
> I just tried to upgrade our Jmol installation to 12.0.18 (binary dow
> Angel, in Wordpress i can use just jmolapplet.jar and i receive
no
> error of reader missing.
Of course. That is the "monolithic" applet that contains all
components. The standard procedure (e.g. when you use Jmol.js and
jmolInitialize() with no special parameters) calls jmolApplet0.jar
w
Angel, in Wordpress i can use just jmolapplet.jar and i receive no
error of reader missing.
Pino
> Wonderful, Pino! Bravissimo!
>
> I'm glad that you could make it work. Congratulations.
>
> It will be appreciated by other users if you write the details
> relevant to how to configure WordPress f
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