Jmol/Visualizing membrane position: Difference between revisions
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You can download the pseudoatom-enhanced PDB file from the server, and then [[Help:Uploading_molecules|upload it to Proteopedia]] for use in a ''Molecular Scene''. | You can download the pseudoatom-enhanced PDB file from the server, and then [[Help:Uploading_molecules|upload it to Proteopedia]] for use in a ''Molecular Scene''. | ||
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 scene shown, using [[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 scene shown, using [[Image:5lil_opm2.pdb]]. | ||
* [http://FirstGlance.Jmol.Org/fg.htm?mol=http%3A//proteopedia.org/wiki/images/d/da/5lil_opm2.pdb View 5lil_opm2.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_opm2.pdb in FirstGlance in Jmol]: Use the ''Ligands+'' button to toggle visibility of the pseudoatoms. | ||
The pseudoatoms have residue name DUM (for dummy atoms). This can be used in the SAT to select them. The red pseudoatoms are oxygens, and the blue pseudoatoms are nitrogens. Thus, coloring them by ''chemical element'' ([[CPK]]) will make them red and blue. | The pseudoatoms have residue name DUM (for dummy atoms). This can be used in the SAT to select them. The red pseudoatoms are oxygens, and the blue pseudoatoms are nitrogens. Thus, coloring them by ''chemical element'' ([[CPK]]) will make them red and blue. | ||
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===Generate the Cylinder=== | ===Generate the Cylinder=== | ||
To 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> | <pre>draw cyl1 cylinder diameter 100.0 color gray (thr607) (leu250)</pre> | ||
Adapt this command to your situation, copy and paste it into the LOWER box of the Console, and click the ''Run'' button at the lower-left of the console box. | Adapt this command to your situation, copy and paste it into the LOWER box of the Console, and click the ''Run'' button at the lower-left of the console box. | ||
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== References == | == References == | ||
<references/> | <references/> | ||
[[Category: BioMolViz]] | |||
[[Category: Macromolecular Assemblies]] | |||
