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@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)