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Using the Richards' Rolling Probe Method,
You Can Derive Volume Information from Any PDB file.

Richards Plot
  • the 3V Volume Calculator
  • the 3V Channel Extractor
  • Download the source code: 3v, v1.2 (.tgz) released on June 2, 2009
    • Cavity Extractor — extracts the cavities for a given probe radius
    • Channel Extractor — extracts a particular channel from the solvent
    • FSV Calculator — calculates the Fractional Solvent Volume
    • Solvent Extractor — extracts the all of the solvent
    • Tunnel Extractor — extracts the ribosomal exit tunnel from the H. marismortui structure
    • VDW Calculator — calculate the van der Waals volume and surface area
    • Volume Calculator — calculate the volume and surface area for any probe radius
  • References:
    1. NR Voss, M Gerstein, TA Steitz, PB Moore.
      "The geometry of the ribosomal polypeptide exit tunnel."
      J Mol Biol. v360 (4): 2006, pp. 893-906.
      download pdf     Pubmed ID: 16784753
    2. NR Voss
      "Geometric Studies of RNA and Ribosomes, and Ribosome Crystallization"
      PhD dissertation, Yale University, 2007 download pdf
  • XYZR example files

Click here for a collection of data and movies from the Exit Tunnel paper (above)
Read the FAQ