<< Plotting Gaussian MO >>
Hi all, I have a cube file with the Molecular Orbitals calculated with Gaussian. When I load the cub file into Chimera, I am only seen half of the orbital surface. I would like to know what should I do to get the whole molecular orbital surface colored (as usually) with only to colors (each on for one half). Regards, Hatuey
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)
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)
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@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
participants (3)
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Elaine Meng -
Hatuey Hack -
Thomas Goddard