Jmol/Visualizing membrane position: Difference between revisions
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Viewing the model in [[FirstGlance in Jmol]], you can use ''Hydrophobic/Polar'' (Views tab) to visualize the domain with a hydrophobic surface. Touching or clicking on atoms at the domain boundaries will identify those amino acids. If you wish, you can center a particular residue, then zoom in, and see atomic detail with ''Vines/Sticks'' (Views tab). | Viewing the model in [[FirstGlance in Jmol]], you can use ''Hydrophobic/Polar'' (Views tab) to visualize the domain with a hydrophobic surface. Touching or clicking on atoms at the domain boundaries will identify those amino acids. If you wish, you can center a particular residue, then zoom in, and see atomic detail with ''Vines/Sticks'' (Views tab). | ||
For 5LiL, I chose thr607.og1 and leu250.cd1. "OG1" means "oxygen, gamma one", namely a sidechain oxygen that is 2 bonds away from the alpha carbon. CD1: carbon, delta one. It would have worked equally well to use the entire residues, simply thr607 and leu250. | |||
===Generate the Cylinder=== | |||
To generate the cylinder in the [[SAT]], click on the button below JSmol ''Advanced: Open JSmol Console''. The command to generate the cylinder will have this form: | |||
<pre>draw cyl1 cylinder diameter 100.0 color gray (thr607) (leu250)</pre> | |||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
