Nonstandard Amino Acids

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This page talks a little about how PyMOL deals with nonstandard amino acids, and the various representations and options available.

By default, PyMOL considers nonstandard amino acids as HETERO atoms. Therefore, when you draw a default surface, the heteroatoms are not included. Also, nonstandard atoms are left out of the backbone representation in the cartoon and ribbon representations.


  • If you're looking to represent the backbone via ribbon or cartoon, then just use the mutagenesis to modify the nonstandard amino acid to something standard, like GLU, or LEU. The draw/ray your structure as needed.
  • If you want the nonstandard amino acid to be included in the surface representation, then set surface_mode to 1. For example, consider the images below. We have a hetero atom shown in the image at left, not included in the surface, become part of the surface when we set the surface_mode to 1.
  • Another work around is to try
flag ignore, bymol polymer, set