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Visualizing Molecular Interfaces

  1. Jun 13, 2012 #1
    Perhaps too subject-specific of a question for this forum but most other bio forums I've seen are molecular-bio oriented whereas this is more of a structural/biophysics question. I've been using PyMol relatively frequently the last couple of years and one area where I've repeatedly been stymied by my lack of knowledge is in understanding how molecules come together. Of particular interest of me are how proteins interact with each other and with ligands. I've tried to gain insight on this topic by trimming out all residues that don't appear to participate in the interaction, but there are still two problems.

    The first is that it's hard to tell which atoms directly participate in the interaction when there is a huge mass of green and blue on the screen (I know you can change the color pattern, but as far as I know there's no way to highlight those atoms participating in the interaction without first knowing what they are). The second problem is that I'd like to actually be able to visualize the molecular surface performing the interaction. I tried using the "surface" command in PyMol but that doesn't do the surface between the two molecules if they are interacting, and it's difficult to visualize the interaction if you show the surface of each component separately.

    Does anyone here happen to know of a good way to clearly highlight the interaction surface for a pair of macromolecules in PyMol or any other visualization software?
  2. jcsd
  3. Jun 13, 2012 #2
    This may or may not work. Never actually tried it precisely as you described it in your post.

    Swiss PDB Viewer has a neat little feature where you can select an atom and then impose a display cutoff at a chosen distance. I used to use this all the time for looking at what residues were near a bound ligand in a protein structure. So, presumably, you can open up your protein-protein model, zoom in on a potentially interesting residue (perhaps identified as critical for protein-protein interaction by some experiments), and then cut out everything within 10 or 20 Angstroms from there.

    Still learning the ins and outs of PyMOL here, so I can't help much on that end. I've gotten complacent with my molecular visualization software over the years. Heh.
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