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jaredsampson / pymolprobity

A MolProbity-style visualization plugin for PyMOL
MIT License
11 stars 3 forks source link

Atom count mismatch #12

Open kexul opened 2 years ago

kexul commented 2 years ago

Hi, I got Atom count mismatch error dialog when running the plugin, step to reproduce: 

fetch 7vth
Run Reduce
Run Flipkin

Environment: Centos 7 Open-source pymol 2.5.0 MolProbity programs installed without PHENIX

Thanks!

kexul commented 2 years ago

The program could proceed when disabling prekin (by renaming the executable file so the plugin could not find it), however.

jaredsampson commented 2 years ago

@kexul Thanks for reporting this. I can reproduce the error with PyMOL 2.5.2 on macOS, and also confirm that it happens with other PDBs as well.

I'm not sure what has changed in the underlying programs and it may take some time to figure out. As a workaround, I was able to get flipkin output (though for some reason the NQH flips do not animate properly) and run probe successfully using the latest binaries available in the Richardson lab's Molprobity repo: https://github.com/rlabduke/MolProbity/tree/master/bin. Flipkin is in that bin directory, and the other 3 programs are in the linux or macosx subdirectories, choose the one for your OS. Please let me know if you have any issues with the workaround.

kexul commented 2 years ago

Hi @jaredsampson, I don't have PHENIX installed. When using the binaries from the Molprobity repo directly, the following error shows in my terminal: 

WARNING:pmg_tk.startup.pymolprobity.main:sh: phenix.reduce: command not found
sh: phenix.reduce: command not found
sh: phenix.probe: command not found
sh: phenix.probe: command not found

And yes, the flipkin and probe output generated successfully, animate not working here too 🤣

jaredsampson commented 2 years ago 
sh: phenix.reduce: command not found

This warning is expected (though perhaps it could be silenced), because the plugin looks for the phenix versions first, and the standalone versions as fallback.

Also, if you need to show flipped NQH sidechains that aren't in the reduce output, as a workaround you can use the MolProbity server to generate the structure of interest with all the desired flips, then load that coordinate file into PyMOL and run probe as you did before for visualization.

jaredsampson commented 2 years ago

And if you want Phenix, the website is https://phenix-online.org/.

kexul commented 2 years ago

Thanks @jaredsampson for the detailed information. I'm happy to try the workaround you mentioned.