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jensengroup / propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
http://propka.org
GNU Lesser General Public License v2.1
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Input file and downloading v3.1 #191

Closed daviddelima closed 1 month ago

daviddelima commented 1 month ago

Hi, I am currently using propka 3.5, I ran propka3 x.pdb and it only provided the output x.pka. In version 3.1, it shows another output file where we can edit the pka and use it as an input to run the calculation again, how do I do that with v3.5?

Second, how do I install v3.1, is it by this? pip install propka==3.1?

daviddelima commented 1 month ago

I was able to install propka3.1 using the command above, my problem is it doesn't respond when I call it using propka or propka3. How do I call it?

sobolevnrm commented 1 month ago

propka3 is the correct way to call the code after installing it with pip: https://github.com/jensengroup/propka/blob/27e0ad2f8d653404f57c78f1cae2ec32cb5adb68/setup.py#L59

Are you in the same virtual environment as you installed the package? Is propka3 in your path?

daviddelima commented 1 month ago

Yes and no. I tried troubleshooting it to put it in the path, but every time I install propkav3.1, it doesn't show in the bins. I also asked you if we can edit the pka input in v3.5, like how it is done in v3.1, as v3.5 doesn't give the other output, only the .pka.

daviddelima commented 1 month ago

I get it know, it's not propka3 but propka31!

sobolevnrm commented 1 month ago

Great; I'm glad this worked out. Thank you for the update!