Nonstandard Amino Acids: Difference between revisions
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(New page: == 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.w...) |
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* 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. | * 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=" | <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: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. | 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. | ||
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rebuild | rebuild | ||
</source> | </source> | ||
[[Category:Biochemical_Properties]] | |||
[[Category:Objects_and_Selections]] | |||
Latest revision as of 21:17, 28 February 2009
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
- 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.
- Surface Mode Examples
surface_mode set to 0, the default. The galactose (blue) is not considered part of the surface.
surface_mode set to 1 -- now including heteroatoms. The galactose and all heteroatoms (blue) are now considered part of the surface and colored blue.
- Another work around is to try
flag ignore, bymol polymer, set
rebuild