Tips for depicting binding pockets?
I am trying to visualize the surface around a bound ligand (binding pocket), in this case within a GPCR. Any tips for doing this? I am trying to mimic some of the features of PyMOL for showing ligand sites. Thanks!
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You can use Visual Preset 6 to automatically represent the binding site as SES, for example:
Visual presets are found in the Visualization menu:
Note that you can create and save your own visual presets: choose selectors (to automatically select specific things in the document), visual models, color schemes and color palettes.
Great, thanks! I will also mess with transparency, etc. in order to see some interactions in more detail.