Structure

1. 01PDB, PDBx/mmCIF and core CIF open as their own tab, drawn in three dimensions beside your sequences — the reader chosen from the file’s contents, never its name
2. 02Chains listed with the kind of polymer each one holds, so a protein-on-DNA entry reads as one
3. 03The residue numbering each chain actually uses, which is the number to quote in a mutation
4. 04The observed sequence per chain, and the construct sequence the file states — the difference is the disorder
5. 05Ligands named by component identifier and counted by copies; waters counted separately
6. 06Modified residues resolved through the file’s own declaration, never guessed from the name
7. 07Temperature-factor range and mean, and colouring by it when the file carries one
8. 08Method, resolution, deposition date, unit cell and space group, quoted rather than computed
9. 09Ensembles: every model, or one at a time, with counts describing one model rather than summed
10. 10Cartoon, sticks, spheres or lines; colour by chain, secondary structure, element, B-factor or N to C
11. 11Highlight a chain, a residue, a range or a component id, with unmatched and unreadable reported differently
12. 12Small-molecule crystal structures too: the symmetry-independent sites, the stated formula, the unit cell and its space group
13. 13A control with nothing to do is disabled with its reason rather than hidden, and reads off rather than claiming to draw

The readers are ours and are graded atom-for-atom against gemmi, the wwPDB’s own structure library, over a corpus of real RCSB entries — coordinates, chain assignment, entry id and resolution all asserted against what gemmi builds from the same bytes. Residue and solvent naming follows the wwPDB Chemical Component Dictionary; for a small-molecule crystal structure the fractional-to-Cartesian matrix is graded against gemmi element by element and site by site, in all three cell regimes, on the convention International Tables for Crystallography volume B states for the Protein Data Bank. Drawing is 3Dmol’s. Everything runs in your browser; nothing is uploaded. The panel runs on @ports/connectors, @ports/macromolecule.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Is my structure uploaded anywhere?

No. The file is parsed and drawn in your browser from the copy stored in your project.

Why does the chain count differ between the PDB and mmCIF copies of the same entry?

Because the two files genuinely say different things. In 1CF7 the atoms are identical, but the PDB copy leaves its ordered waters without a chain identifier while the mmCIF assigns them to chains A-D. Both readings are correct for the file in front of them, and the count follows the file rather than being normalised to hide the difference.

Why can I not colour by B-factor?

Because every atom in that file carries a temperature factor of zero, which is normal for an NMR ensemble or a computed model. There is no B to colour by. The option stays visible and says so, rather than disappearing and leaving you unable to tell that apart from a viewer that cannot do it.

Why is the resolution blank?

Because the entry has none. An NMR structure is not solved at a resolution, and printing 0.00 Å would be a sub-ångström claim. The row shows a dash, which means the file states no value.

Are the waters missing?

They are counted but not drawn by default, because they hide the molecule they surround. The Waters control turns them on, and its count comes from the file. Heavy water is recognised as solvent too, so a neutron structure does not report its deuterated waters as ligands.

Does selenomethionine count as a methionine?

Only where the file says so. A modified residue is resolved through the entry’s own declaration of what it stands in for; where the file makes no such statement the residue is reported as its own component rather than being folded into a standard one on the strength of its name.

Why does a crystal structure show only two atoms?

Because a small-molecule CIF lists the symmetry-independent sites — the asymmetric unit. The rest of the cell follows from applying the space group’s operators, which this viewer does not do, and it says so beneath the scene rather than leaving you to wonder where the atoms went. The formula it reports is the file’s own statement about the whole cell, which is why it can name more atoms than the sites listed.

Two different files are both called .cif. Does it matter?

Yes, and it is why the reader is chosen from the file’s contents rather than its name. PDBx/mmCIF and core CIF are unrelated dictionaries that share the extension: one has dotted tags and coordinates in ångströms, the other underscored tags and coordinates that are fractions of the cell edges. Read one as the other and you get an empty scene rather than an error.

Can I edit the structure?

No — this is a reader. It draws, counts and measures a structure; it does not modify coordinates.