Distributing points uniformly on a sphere

Earlier this semester I had a project where I had to calculate the solvent-accessible surface area of a protein given its 3-dimensional structure (in a PDB file). The suggested method of implementation was to simulate the surface of each atom by distributing 500 points (roughly) evenly across the surface defined by its van der Waals radius. Although that sounds straightforward, it actually took me a while to figure out how to randomly sample points from a sphere defined by a point and a radius.

I did some extensive searching on Google, but most of the methods I found came with the caveat that there would be a greater concentration of points near the poles than at the equator. I finally came across this page, which offered a clear and concise method for sampling points from a sphere.

  • Set up a 2-dimensional coordinate system: the z dimension (running from -R to R, where R is the van der Waals radius) and \phi (longitude, running from 0 to 2\pi radians)
  • Generate random coordinates: z_i \sim \text{Uniform}(-R, R) and \phi_i \sim \text{Uniform}(0, 2\pi)
  • Use the following relation (z = R \sin{\theta} ) to calculate latitude (\theta ): \theta = \sin^{-1}(\frac{z}{R})
  • Finally, convert to Cartesian (xyz) coordinates
    • x = R \cos{\theta}\cos{\phi}
    • y = R \cos{\theta}\sin{\phi}
    • z = R \sin{\theta} = \text{(*gasp!*)} z

Repeat this process 500 times for each atom to simulate its surface!


Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s