Tips for depicting binding pockets?

[Chris 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!

[Admin]

Hi Chris,

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.

[Chris 1]

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