Dear Yura, Thanks very much for this excellent post. I was trying to reproduce this but ran into trouble when adding the hydrogen atoms. You say 'We can easily fix it:' and then applied 'ProtonatePDB'. Could you possibly supply the code for 'ProtonatePDB' or tell me more about it? Many thanks, Linda

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?

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?

Sorry, I can't quite see what's on the screenshot - I don't see the exact URL you are trying to go, and also it seems for me that the green circle in the top right corner indicates you have not the latest version of Chrome. Can you please update it? To take a screenshot you can just press PrntScreen, then Ctrl+V in the e.g. Paint and then save it - it will be the full-screen view.

I might have fixed the link - can you access it now? If it doesn't work, can you try the link directly from the CloudGet? (copy and paste it into the search)

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]

Hello Yury, thank you very much for sharing! I tried to run the example, but get an error message running ConstructPDBSES: NetChain::nnlibunavail: The neural network runtime is unavailable.

Part::partw: Part 1 of {} does not exist.

LinkObject::linkn: Argument LinkObject["C:\Program Files\Wolfram Research\Mathematica\12.1\SystemFiles\Java\Windows-x86-64\bin\javaw.exe" -classpath "C:\Program Files\Wolfram Research\Mathematica\12.1\[Ellipsis] em.class.loader=com.wolfram.jlink.JLinkSystemClassLoader com.wolfram.jlink.Install -init "C:\Users\Micha\AppData\Local\Temp\m-05a497d5-7283-4311-9eef-87cd9588a273",<<4>>,40] in <<1>> has an invalid LinkObject number; the link may be closed.

Do you have any idea what the problem might be and how to fix it? I run M12.1.1.0 on W10

Best regards, Michael

Dear Linda, all the code is published at here (my GitHub repo for the project)