Issues with RNA visualization

[dincarnato]

Hello,
love the idea of this project.
I was trying to visualize PDBs containing RNA chains, but all of them trigger similar errors. See below:

$ proteinview --fetch 2KGP

Error: Failed to open structure file: [StrictWarning: Atoms in Models not corresponding
Atom 860 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 861 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 862 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 863 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 864 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 865 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 866 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 867 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 868 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 869 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding
Atom 870 in Model 2 does not correspond to the respective Atom in the first model.
, StrictWarning: Atoms in Models not corresponding

When pre-downloading the PDB, the viewer opens, but nothing is shown.

Cheers,
Danny

[001TMF]

Hi Danny, thanks for the report and the kind words!

This has been fixed in v0.2.0 (commit 3154043). There were two separate issues:

1. --fetch 2KGP crashing with StrictWarning errors: NMR multi-model PDB/CIF files have different atom serial numbers across models, which triggered pdbtbx's cross-model validation. The parser now uses set_only_first_model(true) to skip all models after the first, avoiding the validation entirely.

2. Pre-downloaded PDB opens but nothing is shown: The viewer only recognized protein backbone atoms (CA) for computing the bounding radius and camera zoom. RNA structures use C4' as their backbone atom, so the bounding radius was 0 and the structure was invisible. This was fixed in a prior commit by generalizing backbone detection to include both CA (protein) and C4' (nucleic acid) atoms.

Both PDB and mmCIF formats now work correctly for NMR structures. We've also added full RNA/DNA visualization support (backbone, wireframe, and cartoon modes with base-type coloring).

Please update and let us know if you run into any other issues!