TreeFam–PDB mapping: pipeline reference

PDB chain → TreeFam sequence → PyMOL, need the residue numbering to survive all 3. Missing residues / partial structures are the annoying bit here. Save for later: same highlight following a residue between sequence and 3D views?

recorded responsibility: core PDB-to-TreeFam mapping pipeline, key-segment identification and PyMOL visualization, within the shared summer 2024 data-engineering project.

repository: treefam-pdb-dataeng. The retrospective summary identifies this repository but does not supply a dated commit or specific module/function for each task.

reference questions: what identifiers join a structure/chain to its protein-family sequence? How are partial structures, missing residues and key segments represented? Which residue-index mapping is used when coloring a PyMOL view? These are questions for inspecting the implementation, not claims that a particular mapping policy was used.

related direction: the same summary records a later transition to Historian evaluation. Keep mapping/visualization outputs separate from inferred alignments or trees used in a benchmark.