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

[Hatuey Hack]

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

On Mon, Jun 9, 2008 at 4:05 PM, Thomas Goddard <goddard at cgl.ucsf.edu> wrote:
> Hi Hatuey,
>
>  If you open a Gaussian cube file containing more than one orbital Chimera
> should open a separate volume for each orbital.  Chimera determines whether
> the file contains multiple orbitals by looking for a negative atom count in
> the first field of the third line (weird format) then after the lines that
> list the atom coordinates there is a single line that names each of the
> orbitals.  Below is a single orbital example.  You can look at your cub file
> in a text editor and see if it matches this format.  If it does but doesn't
> display correctly then I can look at the file if you can put it on the web.
>
>        Tom
>
> Example cube file:
>
>
> azurin 1JZF
> SCF Molecular Orbitals
> -141  -22.336829  -16.222711  -12.353810
>  95    0.436104    0.000000    0.000000
>  83    0.000000    0.436104    0.000000
>  65    0.000000    0.000000    0.436104
>   1    1.000000   12.122777   -2.902144   -5.146283
>   6    6.000000   12.104072   -2.113008   -3.229603
>   ... (removed additional 138 atom lines)
>   1    1.000000   12.112141   -5.890766   -0.172029
>   1 1515
> -1.84745E-19 -2.68150E-19 -3.85426E-19 -5.51630E-19 -7.94108E-19
> -1.16861E-18
> -1.79519E-18 -2.93148E-18 -5.10836E-18 -9.35382E-18 -1.75136E-17
> -3.26273E-17
> ... (removed 86734 additional lines containing density values)
>
>