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Tips for depicting binding pockets?

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    Chris 1
    wrote on last edited by
    #1

    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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      Admin
      wrote on last edited by
      #2

      Hi Chris,

      You can use Visual Preset 6 to automatically represent the binding site as SES, for example:
      0_1645313022471_2492a9c3-00bb-452f-96c0-69d7bf307aab-image.png

      Visual presets are found in the Visualization menu:
      0_1645313044435_6e2231d5-bc1c-4584-94bd-8946a3b2968e-image.png
      0_1645313068970_5ac9b043-90eb-4af0-8810-650fd9d1cb5e-image.png

      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.

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        Chris 1
        wrote on last edited by
        #3

        Great, thanks! I will also mess with transparency, etc. in order to see some interactions in more detail.

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