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 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. | ||
