Protein–ligand covalent bond is not rendered when the protein endpoint is a side-chain atom (1A09)

[ramithuh]

I'm looking at 1a09 and comparing views from pymol, molstar, and 3dmol.js

3dmol.js view - https://3dmol.org/viewer.html?pdb=1a09&select=chain:A&style=cartoon:color~lightgray&select=chain:A;resi:158,178,180,181,182,187,188,203,204,205,206,218,239&style=cartoon:color~lightgray;stick:radius~0.18,colorscheme~greenCarbon&select=chain:C&style=stick:radius~0.22,colorscheme~cyanCarbon&select=chain:A;resi:188&labelres=backgroundOpacity:0.7;fontSize:12&select=chain:C;resi:101&labelres=backgroundOpacity:0.7;fontSize:12

Could be a parsing issue in py2dmol ?

LINK    SG CYS A188 — CF PTH C101    1.80 Å
CONECT  449 1063

Attaching codex's hint at where the bug might happen:

Could the bond be getting dropped while constructing the display representation? py2Dmol appears to parse the CONECT record, but the protein endpoint is CYS SG, whereas protein residues are represented by their Cα positions in the main coordinate map. This may leave the SG endpoint unavailable when explicit bonds are resolved.