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rdk/p2rank
Question about P2rank score/probability cut-off

Hi P2rank team! First of all, I d like to thank you for developing and maintaining such a great tool! As far as I remember, I ve been using P2rank (and fpocket) since 2019 and the experience has been ...
question
  • arnaucoma24
  • 2
  • Opened 
    27 days ago
  • #76

rdk/p2rank
exception in phase 'semantic analysis' in source unit

THis error appears ERROR: BUG! exception in phase semantic analysis in source unit /home/veronica/scipion/software/em/p2rank-2.3/config/default.groovy Unsupported class file major version 65 00032: BUG! ...
question
  • veronicagamo
  • 2
  • Opened 
    on Sep 15, 2024
  • #75

rdk/p2rank
Fail or at least warn users if they try to use wrong combiation of (command,config,model)

E.g. prank rescore -c alphafold should not be allowed.
enhancement
  • rdk
  • Opened 
    on Jun 26, 2024
  • #73

rdk/p2rank
Rescoring of cif files generated by fpocket fails

Hi rdk! I am having an issue with rescoring mmcif files put out by fpocket4. Rescoring here does work for pdb files generated by fpocket, For cif files, however, prank generates an empty rescoring csv. ...
bug
enhancement
question
  • Yorick-126
  • 11
  • Opened 
    on Jun 19, 2024
  • #72

rdk/p2rank
incomplete test_output

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 ...
  • SusuSui
  • 4
  • Opened 
    on Apr 7, 2024
  • #71

rdk/p2rank
Different results compared to PrankWeb?

This is the same/related issue I ve previously asked in the prankweb page however I thought it was useful to ask here as well. https://github.com/cusbg/prankweb/issues/142#issue-2226798402 I am trying ...
  • AlexLam37
  • 2
  • Opened 
    on Apr 5, 2024
  • #70

rdk/p2rank
data input rescore

I get this error when trying to run prank rescore: Dataset must contain protein and prediction columns! What is the format that the input needs to have?
question
  • ClaraVanM
  • 7
  • Opened 
    on Mar 6, 2024
  • #69

rdk/p2rank
Pocket Volume Estimations

Hi, On the webserver there s an easy way to create a task which calculates the volumes of predicted pockets from P2Rank. Is there a way to run these tasks from the CLI? I ve got a population of proteins ...
enhancement
question
  • apl22
  • 2
  • Opened 
    on Feb 23, 2024
  • #68

rdk/p2rank
installation not clear

Hi, I got this error after ./make.sh $ ./make.sh Starting a Gradle Daemon (subsequent builds will be faster) Task :compileGroovy FAILED FAILURE: Build failed with an exception. - What went wrong: ...
  • Canddya
  • Opened 
    on Oct 24, 2023
  • #67

rdk/p2rank
Question about the preprocessing of PDB file.

Hi, Do I need to preprocess the PDB files before running P2Rank, such as adding missing heavy atoms?
  • violet-sto
  • 1
  • Opened 
    on Sep 8, 2023
  • #65
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