Issues

• parsePDB reads plain decimal residue numbers as hexadecimal after a hybrid-36 overflow (writePDB output does not round trip)

  prody/ProDy#2273 · Filter by author dylanpulver opened on Sep 3, 2026

• Numpy version issue for druggability analysis (Drugui 2.0)

  prody/ProDy#2271 · Filter by author stoneandbone opened on Aug 27, 2026
  1

  

• Some tests in test_insty.py timeout when run on a single-cpu system

  prody/ProDy#2236 · Filter by author sanvila opened on Jun 1, 2026
  4

  

• Can't pickle local object 'calcInteractionsMultipleFrames.<locals>.analyseFrame'

  In progress
  prody/ProDy#2192 · Filter by author houyaxuan634-coder opened on Dec 5, 2025
  5

  

• AttributeError: Selection object has no attribute strip and 'strip' is not a valid selection string

  In progress
  prody/ProDy#2188 · Filter by author GCS-ZHN opened on Dec 1, 2025
  1

  

• Not able to install prody==2.4.0 in py3.12.6

  prody/ProDy#2187 · Filter by author parasml opened on Nov 22, 2025
  1

  

• Three-letter code extraction doesn't work in ProDy 2.6.1 under Python 3.12

  prody/ProDy#2185 · Filter by author lokapal opened on Nov 3, 2025
  4

  

• Can Prody parse residue label_seq_id from cif file ?

  prody/ProDy#2180 · Filter by author locitran opened on Oct 11, 2025
  1

  

• Missing key error when parsing PDB entry 7O07

  prody/ProDy#2174 · Filter by author sforli opened on Sep 4, 2025
  1

  

• calcProteinInteractions() throws NumPy UFuncTypeError in ProDy 2.5.0

  prody/ProDy#2142 · Filter by author HaleHasdemir opened on Jul 11, 2025
  7

  

• Problem with calcADPAxes

  prody/ProDy#1975 · Filter by author karolamik13 opened on Oct 15, 2024
  3

  

• ImportError While Using the ProDy Interface in NMWizard

  prody/ProDy#1961 · Filter by author DaddyDaddyFish opened on Sep 19, 2024
  9

• searchPfam fails to parse XML

  prody/ProDy#1933 · Filter by author NicholasMcCarthy opened on Aug 12, 2024
  8

  

• addMissingAtoms PDBFixer fails with InSty/WatFinder tutorial file

  prody/ProDy#1866 · Filter by author jamesmkrieger opened on Apr 16, 2024
  8

• error on tutorial Evolution of sequence, structure and dynamics with Evol and SignDy

  prody/ProDy#1841 · Filter by author Armanda87 opened on Mar 13, 2024
  9

• NMWiz connected chains

  prody/ProDy#1431 · Filter by author dim-99 opened on Dec 8, 2021
  3

• Is there a way to disable logger output in notebook?

  prody/ProDy#1401 · Filter by author zllion opened on Aug 3, 2021
  14