Nonstandard Amino Acids

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Overview

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.

Workarounds

flag ignore, bymol polymer, set
rebuild
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