3D Polarization (Thole)

How can you determine what the computer calls the x, y, and z axis?

Hi,





The usual notation is x for the first, y for the second and z for the last, third coordinate. However, as the internal structure of a molecule is independent of the translation and rotation cyclic changes in this order, as y, z, x and z, x, y will lead to the same structure while other reordering results in a mirror image, an enantiomeric structure. Also, simply rotating the molecule in a viewer and saving it does not necessarly change the coordinates.





I hope this helps.





Best wishes,





Ödön

Jpurdon wrote:

How can you determine what the computer calls the x, y, and z axis?

If you don't know what the X, Y, and Z axes are, then it seems like the XX, YY, and ZZ polarization tensor values can't really be used without that critical information.





When you have a symmetric molecule, intuition can be used to determine the axes. However, as the molecule becomes more complex, this guessing method becomes too difficult. No matter how the molecule is oriented in the viewer, the program calculates the same XX, YY, and ZZ polarization tensor values, so it must go through an algorithm to assign specific axes. Because of this, is there a way to figure out what the computer is thinking? Since it's always the same, a great feature for the future would be to overlay a cartesion coordinate system on the molecule, since the computer calculates the same values already.





also, someting did change between version 4.0.4 and 4.1.14:





some of the x,y, and z values switched palces, but appear to be constant within each version.

I may have answered my own question, and am looking for confirmation.





When you hit "display" for 3D polarization, and the dual window pops up with the molecule on the left side and the charge cloud on the right side, the program always orients the molecule a certain way. It appears that "x" is left-right , "y" is up-down, and "z" is out of the page, relative to this initial position, before clicking on it and moving it around. Is this correct?

Quote:

When you hit "display" for 3D polarization, and the dual window pops up with the molecule on the left side and the charge cloud on the right side, the program always orients the molecule a certain way. It appears that "x" is left-right , "y" is up-down, and "z" is out of the page, relative to this initial position, before clicking on it and moving it around. Is this correct?

Dear Joe,





yes, this is correct, and (0, 0, 1) is looking to be nearer than (0, 0, 0).


We'll definitely add the displaying of the coordinate system to the 3D viewer.





Kind regards,


Judit

Thanks for the quick responses!

Dear Joe,





displaying the coordinate system in MarvinSpace will be available in Marvin 5.0.2 coming in the days.





Kind regards,


Judit