Jmol/Visualizing membrane position: Difference between revisions
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In the case of 5LiL, I had difficulty getting the pseudoatoms to show from a green link (even though they displayed in the [[SAT]]). In the PDB file, the pseudoatoms followed a MASTER record. I deleted the MASTER record and all CONECT records, and then I got the results shown above with [[Image:5lil_opm2.pdb]]. | In the case of 5LiL, I had difficulty getting the pseudoatoms to show from a green link (even though they displayed in the [[SAT]]). In the PDB file, the pseudoatoms followed a MASTER record. I deleted the MASTER record and all CONECT records, and then I got the results shown above with [[Image:5lil_opm2.pdb]]. | ||
* [http://FirstGlance.Jmol.Org/fg.htm?mol=http%3A//proteopedia.org/wiki/images/d/da/5lil_opm2.pdb View 5lil_opm.pdb in FirstGlance in Jmol] | * [http://FirstGlance.Jmol.Org/fg.htm?mol=http%3A//proteopedia.org/wiki/images/d/da/5lil_opm2.pdb View 5lil_opm.pdb in FirstGlance in Jmol] | ||
==Methods: Translucent Cylinder== | |||
===Choose boundary residues=== | |||
First you must choose residues or atoms in the model that are closest to the ends of the desired cylinder. If you wish, you can use a pseudoatom-enhanced model to assist. | |||
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). | |||
</StructureSection> | </StructureSection> | ||
== References == | == References == | ||
<references/> | <references/> | ||
