Hello Michael, Did you install Cygwin (mentioned at the beginning of the examples)? It's just that I run the same configuration and it works fine.

Thank you! I am familiar with the pymol, and yes, this is the same surface that pymol creates. Here the benefit is that you get not only the 3D picture but also coordinates of all vertices and the information on how they are connected, so you can not only look at it but try to use these data for further computations.

Sounds great!

About reproducing the results - .wl is meant to be imported with the CloudGet - theoretically, you shouldn't bother with anything. These lines work for me:

CloudGet[CloudObject["https://www.wolframcloud.com/obj/polyachenko.yua/Published/ConstructPDBsurfaces.wl"]]; pdbName = "1aki"; pdb = DownloadPDB[pdbName]; pdbProtonated = ProtonatePDB[pdb]; DrawPDBSAS[pdbProtonated]

hmm, that's strange - I can open it in the incognito mode. Can you please send a screenshot of the problem (error)?

I've just double-checked it on Win10 - it works for me. Did you install Cygwin?

Dear Linda, thanks for your interest.

The code can be downloaded from here - it's actually just the link from the CloudGet. The code is a wrapper for the reduce program. It takes your PDB in a string form, saves it to a file, runs Reduce on it, loads the new protonated PDB in a string form, and returns it.

What trouble did you run into? Did you get an error? What OS do you use?

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