rdk

Hi, unfortunately this is not possible at the moment. The volume calculation you see on prankweb.cz is actually done in the browser and is not part of P2Rank. A quote...

Closing since the question was answered in PrankWeb issue. If some confusion remains, let me know.

You can find exemple dataset files in [test_data](https://github.com/rdk/p2rank/tree/develop/distro/test_data). In particular: [fpocket3.ds](https://github.com/rdk/p2rank/blob/develop/distro/test_data/fpocket3.ds) and [concavity.ds](https://github.com/rdk/p2rank/blob/develop/distro/test_data/concavity.ds). There is one column (`protein`) for original structure file and another (`prediction`) for a file with pocket...

fpocket should work, although I haven't tested it with 4.x versions. Are you using the latest version of fpocket? If you try it please let me know if it works....

Looks like there is a bug that needs to be fixed. Could you attach fpocket output files that are giving you the error, at least for 1a28? > But then...

@ClaraVanM sorry for the delay. If it is still relevant, you can try if the release 2.4.2 (https://github.com/rdk/p2rank/releases/tag/2.4.2) works in your case. It containes updated support for loading fpocket predictions....

That depends. P2Rank tries to disregard/ignore all the ligands before running prediction. Ligands attached to peptide chains should also be ignored, as long as they are stored in the PDB/CIF...

Thanks for adding clarification. I see a lot of sense in having this implemented in P2Rank. (2) Regarding cofactors: so you’d like an option to "consider specified cofactors as part...

(2) Ok I'm going to implement this. Will you be able to help me with testing? P2Rank doesn't use fpcocket by default. That is, if you run `prank predict` fpocket...

Hi [bbu-imdea](https://github.com/bbu-imdea), thank you for provining more details and examples. I'm already working on P2Rank updates: a) custom modified amino acid mappings with pdbfixer preset and b) ability to define...