Nathaniel Corley comments

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                                            Nathaniel Corley

Determinism when resolving atom alternative locations

Hi, Yes, we definitely need the `set()` since we're storing one `altloc` ID per atom, and thus have duplicates within a residue. Enveloping with `sorted()` should be a quick fix....

Bonds cannot be found for alternative atom names

I can pick this up -- will try and open a PR within the next week

Using Modelforge -RF3 to test protein folding of sequences containing D-residues in main chain.

That is correct, if it has a defined CCD code, we will load the appropriate streochemistry

Input direct from PDB file fails

Thank you for raising this issue! We're aware and looking into it; we'll have a patch soon

Add `atomworks` to extension package page

We'd be thrilled! We will circle back after a few more days of cleanup so we can integrate when our API's stabilize

fix: support alternative atom names within connect_via_residue_names

@Croydon-Brixton welcome your thoughts, as I know you've thought a lot about this as well

fix: support alternative atom names within connect_via_residue_names

> I found a problem with residues with mixed naming standard: For about 50% of all residues in the CCD there are conflicting names between standard and alternative, i.e. the...

fix: support alternative atom names within connect_via_residue_names

Updated to address the comments; given that we only lookup alternative atom names in the rare event that we can't match all of the atoms to standard names, I thought...

fix: support alternative atom names within connect_via_residue_names

Thank you for the feedback, and apologies for the delay — I will update and re-submit this weekend!

fix: support alternative atom names within connect_via_residue_names

Closing since in the latest updates of the PDB they no longer have outdated atom names