Editing Nonstandard Amino Acids (section)

=== 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]]