VMD-L Mailing List

From: Luis Guillermo Cota Preciado (lgcota_at_gmail.com)
Date: Thu Jul 01 2010 - 18:10:10 CDT

Here's a couple of questions whose answers I haven't been able to come up
with myself:

   - At least on my screen, when VMD is in perspective mode atoms (spheres)
   become oblong as they get closer to the edge of the window. How can I
   correct this
   behavior?
   - In trying to replicate a color with its RGB values (divided by 255 in
   order to get the fractional number) I find out that I get very different
   results as those wished. Particularly, I am having trouble with the
   yellow-orange range. Also, the "Color Scale" sliders don't seem to have any
   effect on the color of the selected atom type, for example. How can I adjust
   a color's brightness and saturation?
   - Default (VDW) values for Si and O radii are 2.1 and 1.62 Angstroms,
   respectively, whereas the Si-O bond length is 1.6 Angstroms, approx. Even
   so, the Si-O bond seems to be much larger than the individual atoms in the
   CPK representation, with Sphere Scale set to 1. In other words, what is the
   real scaling factor for atoms in the CPK representation? (It is obviously
   much less than one.)

Thank you very much in advance.