I need to find teh hydrodynamic and/or the Stokes radius of histamine, aspirin and cefazolin. I don't have a good understanding on how can I use the information given in the geometry window to calculate it. The ? buttom explains about the radius in the surface are is given. Can I jus use the area and find the radius of that circle? Also, there are a green and a yellow circles, which one should I use. Can I have more explanation on the values and how can I use them in my case?
I'm afraid that your enquiry is not related to our Geometry calcuations thus we cannot help you.
The radius (minimal or maximal projection) has no connection to the Stokes radius, as our radii are purely computed from the molecular geometry of the lower energy conformer. The radii are computed in 2D for the projections which show maximal or minimal projection area.
Can I calculate the radius of the given molecule using the polar area? I just need the hydrodynamic radius of a molecule, do you have any input on that? I cannot find any paper with that information. My molecules are histamine, aspirin and cefazolin.
No, radius is calculated for the whole molecule.