Add hydroxyproline hyp as aa#550
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Adds Phase 5.2 as a new in-scope item with per-PR disposition matrix: - #640 FindXDR refactor: investigate-then-close-or-rebase (XDR may be gone post-Phase-4) - #600 Travis-CI integration: close .travis.yml part (Travis dead), cherry-pick 4 orthogonal files - #554 Omega torsion: extract C++ slice (residueRotamerSet, residue.C), defer .sip to Phase 6 - #550 HYP residue: rebase + merge in v1.6.1 (no Python parts, pure C+++data gap fix) - #546 Insertion code printing: extract C++ slice (residue.{h,C}), defer .sip to Phase 6 Plan breakdown (A/B/C/D) sequenced to avoid residue.C merge conflicts (C bundles #554+#546; D HYP runs after C OR merges into it). Release criterion 4 added: each open PR must reach a recorded disposition. Open question 3 added: XDR-still-used grep verifies #640's path. Open question 4 added: maintainer policy on cherry-picking from departed contributors. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Hello,
we are working with collagens on our end that are full with hydroxyproline and are represented only as unknown/? proteins for which no torsion angles are returned. This is somewhat unfortunate and from what we grasped so far we hence need hydroxyproline added as part of the standard repertoire of residues - it appears in 157 entries in PDB and some sources, sadly I found none on the PDB site, claim that HYP should be understood upfront and not need any separate definition. The patches provided shall be sufficient to have HYP accepted in ATOM lines.
At some point we also need to build peptides with HYP - well, regular PRO would be fine. I had thought that this might just be a variant of PRO and performed respective changesto the PRO.db file, i.e. I introduced the extra oxygen at the position of 2HB and ... not knowing any better, please help, just placed another hydrogen a bit off. Connections were created. Nodes deleted. I just have no clue whatsoever if the link from HYP in a PDB ATOM line to that variant of PRO would be made at all.
Hoping for you all to like this challenge for one reason or another and chime in,
best,
Steffen