Biological Unit: Showing
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This article explains how to show a biological unit (biological assembly) from a green link in a scene in Proteopedia. If you simply want to see a biological unit, go to Visualizing the Biological Unit. For background, see Biological Unit and Asymmetric Unit.
Biological Unit 1Biological Unit 1
Proteopedia, using JSmol, is able to construct biological units. When you are developing a scene for a Proteopedia green link, using the Scene Authoring Tools with a published PDB code, you have the option of loading either the asymmetric unit or biological unit 1 (the "biological assembly").
Biological Unit 2 or HigherBiological Unit 2 or Higher
Occasional PDB files specify more than one biological unit. The easiest way to see all the biological units is to use FirstGlance in Jmol: see Visualizing the Biological Unit.
If you want to show biological unit 2 (or a higher number) in a green link scene in Proteopedia, use the FILTER option in the Load Molecule dialog of the Scene Authoring Tools. Biological units are designated as "biomolecules" in PDB files. To get biomolecule 2, simply enter biomolecule 2 in the FILTER slot. This will load all atoms in biomolecule 2.
SimplificationSimplification
Sometimes there are too many atoms for good performance of JSmol, and in such cases, simplifying to show only the alpha carbons (or sometimes a subset of alpha carbons) is usually sufficient. Consider the biological units ("biomolecules" in PDB nomenclature) in 7r1c, a bacterial gas vesicle. Its asymmetric unit contains a single protein chain with 65 amino acids (alpha carbon atoms) and 496 atoms (hydrogen atoms were omitted).
| Biomolecule | Chains | Alpha Carbons | All Non-Hydrogen Atoms |
|---|---|---|---|
| 1 | 5 | 325 | 2,480 |
| 2 | 100 | 6,500 | 49,600 |
| 3 | 930 | 60,450 | 461,280 |
The performance of JSmol becomes sluggish with >30,000 atoms, and very sluggish with >100,000 atoms. FirstGlance simplifies the 930-chain biomolecule 3 of the 7r1c gas vesicle to every 3rd alpha carbon. In order to show the simplified model as a solid object, the "spacefilling" radii of the alpha carbons is expanded to 6.0 Å. The radius assigned to the alpha carbon atoms in models simplified by FirstGlance is reported when you click Solid in the Views tab.
Alpha Carbons OnlyAlpha Carbons Only
In order to load only the alpha carbon atoms, begin the FILTER with *.CA;. So, for example, the FILTER for biological unit 2 of 7r1c would be *.CA;biomolecule 2;.
...UNDER CONSTRUCTION