Re: [Jmol-users] Changing the phase of a signed surface?

[Pshemak M. <pm...@ch...>]

  On 10/10/2011 2:46 PM, Rzepa Henry wrote:
> I am loading two  MO surfaces thus
>
> load HHa_mo15.xyz;isosurface HHa_mo15.jvxl translucent;isosurface append HHa_mo17.jvxl translucent;
>
> I want to show the overlap between two  MOs.  It is of course a  50% probability that the phases will match to show the effect I want.  Can anyone offer a solution to inverting the phase of one of the  MOs if it turns out wrong (i.e. change red to blue and vice versa for just one of the surfaces?)

I believe specific listing of colors will do the trick: phase color red 
blue vs phase color blue red.


> And this is pushing it rather!  If the two surfaces do overlap with the same phase,  does any code exist to tell me the overlapping volume  (or if the phase differs, the negative overlap volume?)
>

I am not sure if that is what you have in mind, but there is linear 
combination of MOs possible (in the manual under "mo", example 48 at 
http://chemapps.stolaf.edu/jmol/docs/examples-12/new2.htm  ).

Regards,

PM