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What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated.

I'd prefer the output to be a watertight triangle mesh of the protein surface. Also, I'd like the tool to be scriptable (i.e. no need to open a GUI).

So far, I've been playing with MSMS and EDTSurf. But I was wondering what was standard in research, as well as if there was anything in the standard bioinformatics libraries.

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    $\begingroup$ Do you want to visualize the protein surface or the electron density map? (PyMOL can do both.) $\endgroup$ – user37894 Feb 15 '18 at 18:16
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PyMOL and Chimera can do that, and both can be script-driven. The PyMOL wiki is full of examples, and probably already has some how-to that would get you started. Chimera also has a complete documentation.

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