At here, I color residues 200 to 350 from red to white to blue in the surface view. One also color the object in other modes. Others are not affected.Ĭommand: spectrum count, red white blue, 7D47 and resi 200-350 Out of the box stunning transitions when changing data, updating colours. Use red to white to blue to present gradient colors for a selected region (residues 1 to 60). The Jmol application is a standalone Java application that runs on the desktop. The colors are distributed from the first to the last residues evenly.Ĭommand: spectrum count, red white blue, 7D47 and resi 1-60 From N-term to C-term of the object.Ĭommand: spectrum count, red green white cyan lime forest orange blue, 7D47Ĩ colors are chosen to color the papain-like protease. I am showing several examples below and the colors, in particular gradient colors, are very useful to present research works. There are advanced ways to illustrate objects in user-defined color scheme using “spectrum” command. Because the N-terminus of a peptide chain is distinct from the C-terminus. N-term is blue, C-term is red and middle colors vary. The color shaded rectangles in the lower structure define these regions. We can choose “spectrum” and “rainbow” to have whole protein (object) colored like the figure below. To color an entire structure from N-terminus to C-terminus as a rainbow, go to Polymer under the Components Panel. PyMOL provides coloring function on right of object panel. The default color is green, ions are illustrated in separate colors (here: gray: zinc, green: calcium). You can explicitly assign atom colors to elements using JavaScript standard color names, octal equivalents, or RGB triples. Here is a step-by-step example to have “rainbow” color, using SARS-CoV-2 Papain-Like protease determined by my group (PDB ID: 7D47).Ībove figure shows the default color and secondary structure presentation by PyMOL 2.0 or newer. You can change the default either to the Rasmol 'CPK' standard or the Jmol standard, or you can customize any specific element's color. It is planned that a future version of Proteopedia will provide a mechanism to place a color key in the legend or caption beneath the molecular scene in Jmol (. Interaction of the complexin accessory helix with the C-terminus of the. The rainbow color begin with blue at the N-terminus to red at the C-terminus. doi:10.1016/j.jmb.2006.07.018 Bin, L., Song, S. The convenient way is using the “spectrum” function to have “rainbow” colors for the object. This can use various combinations of commands (you may want to consult the Jmol Interactive Scripting Docs ). Most new PyMOL users like to color the protein/DNA/complex object with multiple colors. Open the scripting window of the applet for command entry. then check colors below to spacefill residues: 1, 2, 3, 4, 5, 6, 7, 8, 9. Jmol has several common Display Color options to make your model look visually pleasing or to indicate specific features of the molecule.
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