![]() An Introduction to Jmol Scripting - Very helpful interactive tutorial that lets you click buttons to see how different command lines change the appearance of a 3D structure.for "someColor." I've found that when using the PDB Jmol window, it helps to start the command with color_by_chain Substitute red, blue, yellow, orange, etc. ![]() This selects a single contiguous peptide in multi-part protein complexes. color_by_chain select :chainLetter color someColor - Change the color of a subunit/ chain.String together multiple commands by using a semicolon. Replace someNumber with a value of at least 50 (50 RasMol units = 0.2 Å). wireframe someNumber - Displays all atoms/bonds as sticks.Replace chainLetter with the appropriate chain letter (e.g., display 53-95:B) Replace the #'s with the range of amino acid residues. display #-#:chainLetter - Allows you to display only a sub-section of the structure while hiding the rest of it.Replace someNumber with a value from 1 - 100. spacefill someNumber% - Displays all atoms as spheres.Useful if you still have the backbone displayed, or if ligands are buried inside the structure. color isosurface translucent - allows you to see through the surface into the molecule.Replace someColor with the name of a color. color isosurface someColor - Changes the color of the surface. ![]()
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