New User Problems

Hey Guys,

I'm having some issues with the program for Mac OSX. I'm a undergraduate student in biology and I was just exploring photosynthesis so I decided to try to make a 3d model of Chlorophyll-a. I finished the model, but i'm having trouble displaying the electrostatic potential surfaces. This issue is not unique to my chloroplast model, it also occurs with the example models included. When I calculate the surfaces, it displays them only incompletely(some surfaces are not colored). In addition, my chloroplast seems to appear in solid green(I assume there are electrostatic potential differences within chloroplast, right? ) I've included an image of the surface map, as well as the ball and stick model in case the problem is with my construction and not the program itself. Any help you could provide would be well appreciated. Thanks.

-Noah Brett

I’m having some issues with the program for Mac OSX. I’m a undergraduate student in biology and I was just exploring photosynthesis so I decided to try to make a 3d model of Chlorophyll-a. I finished the model, but i’m having trouble displaying the electrostatic potential surfaces.

The first thing to realize is that the ESP surfaces are evaluated on the van der Waals radii. So if you’re displaying vdW spheres (as you did in your screen shots), you won’t see much of the surface – the two will have the exact same radii and will “compete.”

In addition, my chloroplast seems to appear in solid green(I assume there are electrostatic potential differences within chloroplast, right? )

The ESP is evaluated using the Gasteiger charge model. Since I don’t have the molecule on your screen, I don’t know for sure, but I suspect that the Gasteiger model is having issues with the metal complex.

If you run a quantum calculation of any sort (e.g., MOPAC) the ESP can be evaluated from the quantum result, and will thus be a much higher accuracy description of the real electrostatic potential around the model.

-Geoff