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2014-03-28T02:00:24Z

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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 [http://en.wikipedia.org/wiki/Amino_acid#Nonstandard_amino_acids 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 ===
* 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|surface representation]], then [[surface_mode|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.

<gallery caption="Surface Mode Examples" heights="200px" widths="200px">
Image:sm0.png|[[surface_mode]] set to 0, the default. The galactose (blue) is not considered part of the surface.
Image:sm1.png|[[surface_mode]] set to 1 -- now including heteroatoms. The galactose and all heteroatoms (blue) are now considered part of the surface and colored blue.
</gallery>

* Another work around is to try
<source lang="python">flag ignore, bymol polymer, set
rebuild
</source>

[[Category:Biochemical_Properties]]
[[Category:Objects_and_Selections]]

Nonstandard Amino Acids - Revision history

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