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[WSS20] Constructing protein surfaces

Posted 5 months ago
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13 Replies

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Posted 4 months ago

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?

Posted 4 months ago

HI Yura, Thanks for the very prompt response. Unfortunately, the link you gave is perhaps in your personal area and says that I don't have permission to access the item - can you alter this? I run Windows. Thanks again, Linda

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?

Posted 4 months ago

I hope you can access a screenshot of what I see on clicking the link. WOLFRAM CLOUD Http Error Code 403 and 'Sorry, you do not have access to this item.

Attachment

Attachments:

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)

Posted 3 months ago

Thanks very much again Yura. The link now downloads but I cannot confirm it works for me yet as I am not familiar with .wl files, so some learning. The latest version of cygwin would not install but I did manage to get a previous one to run. So I should be all set and look forward to reproducing your post as well as try some other proteins. Thank you so much.

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]

Wow this is cool, looks exactly just like in Pymol, I don't know if you are familiar with it, but it looks great. With can you see also the active site of a protein. Cool!

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.

Posted 1 month ago

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

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.

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