Yooshin Kim

@aniketpati1121 while the issue itself is simple, I think it needs reviews or decisions from contributors.

Thanks. didn't know about hybrid36 format. However, OpenMM seems to use hexadecimal (base16), not hybrid36 format (base 36). ([openmm/openmm#3501](https://github.com/openmm/openmm/pull/3501) and [openmm/openmm#3522](https://github.com/openmm/openmm/pull/3522)) (in [openmm/openmm#659](https://github.com/openmm/openmm/issues/659) mentioned in [#1897](https://github.com/MDAnalysis/mdanalysis/issues/1897), they ended up implementing...

> > Letting Universe `__init__` to accept optional parser (TopologyReaderBase) argument, so that users can provide custom parsers for non-standard formats, could also solve this issue. > > You can...

> 0. Performance isn't affected for standard complying PDB parsing I ran a simple benchmark test for hy36decode. Using hy36decode for decimal numbers does make the parsing about 2.3 times...

@marinegor I think you can just use water molecules in with resid >9999 if you want to use it as a test data. [1f0u_solv.pdb](https://github.com/user-attachments/files/23436285/1f0u_solv.pdb)

@marinegor Thank you. There seems to be 814 HOH residues with hex resids, so it checks out. And [Gemmi](https://gemmi.readthedocs.io/en/latest/mol.html) seems to use hybrid-36, so probably can consider this issue as...

@marinegor Yes I think so, while I only looked at parts related to PDBParser. It would be also good to explicitly mention or suggest to use the gemmi MMCIF parser...