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rdk / p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

Home Page:https://rdk.github.io/p2rank/

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incomplete test_output

SusuSui opened this issue · comments

commented

Hi,
I tried running p2rank from bash. I added a pdb file to "test_data". However, for "test_output" I did not receive the "structure.pdb_predictions.csv", "structure.pdb_residues.csv". In the "visualizations" I did receive the structure.pdb.pml. When I run the exact same file through PrankWeb I received them. Would you have any idea why it is like that?

Thanks in advance!

commented

Hi,
Which version of P2Rank are you using? Is it downloaded from https://github.com/rdk/p2rank/releases or built from sources?

commented

It was downloaded from that url and the version is the latest 2.4.1

commented

Unfortunately I wasn't able to reproduce it. Could you provide more details?

  • What operating system are you running on?
  • What is the exact command that produces this behaviour?
  • If you can, provide the structure file itself
commented

Hi I tried running it on a different machine and it worked there. That means there has to be some internal problem with my machine which is not connected to the program. I will try to resolve it. Anyways thank you for the help!