PDB 3D Viewer
Analizza strutture proteiche da file PDB: parser testuale, statistiche atomi/residui/catene e formula molecolare. Nessuna libreria 3D - la struttura non lascia il browser.
Carica struttura
Bioinformatica Strutturale - risorse per studenti IT
Questo tool supporta studenti dei corsi in bioinformatica strutturale di:
- Tor Vergata - corso magistrale Bioinformatica con laboratori strutturale
- Sequence Alignment Viewer - visualizza allineamenti FASTA e CLUSTAL
Approfondisci la teoria con la serie UniAppunti / Bioinformatica.
Come utilizzare PDB 3D Viewer
Load a structure
Insert a 4-character PDB ID (e.g. 1AKE, 4HHB) and download from RCSB, or load a local .pdb file (max 50 MB), or press "Load Example" for a small test structure.
View statistics
The tool automatically calculates atomic totals, unique residues, present chains, and aggregated molecular formula from the ATOM/HETATM lines.
Filter atomic table
Constrict table by chain and/or residual name, then navigate through pages (50 atoms per page).
Go to 3D view
Explore the interactive 3D structure by clicking on the direct link to RCSB PDB or use Mol* (molstar.org) or PyMOL: this tool only provides text analysis.
Suggerimenti
- Use "Load Example" to see 5 atoms of Alanine (ALA) and understand how to read the table before loading a real structure.
- Filter by chain when analyzing complex multi-subunit structures (e.g. oligomers or heterocomplexes with multiple chains).
- The aggregated molecular formula reflects only the atoms present in the ATOM/HETATM lines of the loaded file: hydrogen atoms often not resolved by X-ray are not counted.
Domande frequenti
Does the tool show a 3D visualization of the protein?
No, it's a text parser and analyzer of the PDB format: reads ATOM/HETATM lines and extracts data and statistics, but does not render 3D models. For interactive visualization use the links provided at molstar.org or PyMOL.
Where are structures downloaded from when I enter a PDB ID?
From RCSB PDB (files.rcsb.org), the official global database of protein and macromolecular structures, via the public .pdb file associated with a 4-character ID.
What data is extracted from each row ATOM/HETATM?
Serial number, atom name, residue name, chain, residue sequence number, coordinates X/Y/Z in Angstrom and element symbol, reading columns fixed by the PDB format.
Is the file I'm uploading sent to a server on this site?
No, parsing of the .pdb file occurs entirely in the browser. The only network request is a direct download from RCSB when using the search by PDB ID; if you load a local file, its content never leaves the device.
What are the file upload limits?
Only files with a .pdb extension and a maximum size of 50MB are accepted; larger files or those with different extensions will be rejected with an error message.