Oliver Beckstein

Would it help in any way to skip tests such as `test_thread_limit_apply` https://github.com/MDAnalysis/mdanalysis/blob/519ac568252857b10fb37c8f1b37c3c157c0df7d/testsuite/MDAnalysisTests/transformations/test_base.py#L93 in environments where only 1 CPU is available?

@lilyminium do you know if this issue is related to the switch-over to the new guesser system?

@ricard1997 , which program and force field generated your file? Do you have a topology file (e.g., PSF or TPR) that you could use?

Looks useful!

Hi @jomimc , PDAnalysis looks very interesting. As it is, it unfortunately does not meet the criteria for inclusion in the [MDAKit registry](https://mdakits.mdanalysis.org/mdakits.html) because your tool does not use MDAnalysis,...

@Aryaman-Chaudhri , personally I am not currently using/needing LDDT so I won't be reviewing any code outside of MDAnalysis. If you're opening a PR for MDAnalysis then I'll be involved....

If you look at #1897 and PR #1978 then I'd say MDAnalysis already supports hybrid36 PDB format. Or is what you're looking for not "hybrid36"?

> 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 always provide a...

If I read your issue and the linked openmm issue/PR correctly then you're really asking for supporting reading of VMD-style hex numbered PDBs, right? > I don't think it is...

Thanks for digging through all these old discussions. Amongst them was the comment https://github.com/MDAnalysis/mdanalysis/issues/1897#issuecomment-401818711 > Does it make sense to allow this format also for residue ids? The purist in...