Select ligand and _C color atoms opaque # carbon atoms of ligand in purple Select ligand spacefill 0.6 wireframe 0.3 # ligand in ball and stick Select water spacefill 0.2 # water oxygens as spheres Set ssbondsbackbone false # disulfide bonds between sulfur atoms, not C-alpha Select backbone wireframe 0.3 # but thick bonds for main chain Select protein wireframe 0.1 # thin bonds for protein Below are the commands to show the hydrogen bonds in the context of the protein, ligand and water. For the other green links in the section, I was able to use the the conventional method because the command "set picking center" had already been issued. Set picking center display all script /scripts/37/376372/Hbonds/5.spt Įxcept for the two Jmol commands that are explicitly shown above, the rest of the figure was saved as the usual state file in the scene authoring tool, and then called to generate the figure ("script. To enable centering with the mouse for this scene ("set picking center"), the green link was made as a JmolLink rather than using the Screen Authoring tool. Here is an animation to see what the commands doĪnd a screen shot of the finished scene with captions for reference Select cys.sg wireframe 0.25 set ssbonds backbone #disulfide bonds Hover "%n %r, Chain=%c, Element=%e" #show 3-letter code number, chain and element Label "%m" set labelOffset 0 0 color label yellow #.with yellow labels on top Select *.CA spacefill 0.8 #spheres on alpha carbons Select protein backbone 0.4 color backbone group #rainbow c-alpha trace Select ligand wireframe 0.3 spacefill 0.5 #make bonds on ligand a bit thicker This is a script to create the opening scene after loading coordinate 1HEW (you could also use the screen authoring tool) How some of the figures were made Opening scene 3.7.10 hydrophilic residues and proline.3.6 product complex with five sugar units.2 Substrate complex with sugar not in chair conformation.
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