[Chimera-users] << Plotting Gaussian MO >>

[Elaine Meng]

Hatuey and Jonathan,
It sounds like you can just open the cube file one time and Ctrl- 
click on the histogram so that there are two contour levels.  You can  
color each isosurface differently even though you just have one copy  
of the data open.

This recent message explains how to undisplay the box that appears  
when you have negative contour levels:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-June/002688.html

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Jun 9, 2008, at 2:35 PM, Hatuey Hack wrote:

> Hi Tom and Jonathan.
>
> Thanks by your answers.
>
> Tom, my cube file begins as you said (see below). As it has 30MB (I
> compacted with ZIP and RAR but get a 7MB file!) I could not send to
> you.
>
>  Opt-Freq mo=67
>  Alpha MO coefficients
>   -34  -19.025542   -8.992895   -7.648475
>   234    0.166667    0.000000    0.000000
> ......
>
>
> Jonathan,
>
> I load the map twice. In the first control window, I stay at the left
> (negative value) of the histogram and in the second, I stay at the
> right (positive). Now, I can see both part of the orbital but I also
> see a box (from the negative value) that make the surface difficult to
> see.
>
> Also, I did not see any atoms
>
> Regards,
>
> Hatuey