I want to read a PDB file and display/render the atoms using a graphics engine.

If I consider each residue in the protein as a solid sphere, what would be the radius of the sphere?

How can I calculate it? Or, is there any database for that?

  • $\begingroup$ You may want to check how existing molecular viewers (PyMOL, Jmol, Chimera, web-based viewers on RCSB, PDBe and PDBj websites) render it. $\endgroup$
    – marcin
    Jun 27, 2022 at 12:23
  • $\begingroup$ @marcin, I am developing my own software for learning ourposes. $\endgroup$
    – user366312
    Jun 27, 2022 at 12:30
  • $\begingroup$ Van der Waals radii are used to construct a special kind of molecular model called a space-filling model. These models are constructed by drawing each atom as a van der Waals sphere with the atom’s nucleus at the center of the sphere. taken from reed.edu/chemistry/ROCO/Geometry/space_filling.html not sure how to expand it to a full residue $\endgroup$
    – pippo1980
    Jun 27, 2022 at 12:36
  • $\begingroup$ @pippo1980, thanks! good information. :) $\endgroup$
    – user366312
    Jun 27, 2022 at 12:39
  • $\begingroup$ try this paper not sure why 5A radius is choosen researchgate.net/figure/… the picture seems OK to me tough $\endgroup$
    – pippo1980
    Jun 27, 2022 at 12:40


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