MolDraw › Chemistry tools › PDB Viewer Online

PDB Viewer Online

In short: Open a protein structure from a PDB ID, a .pdb, mmCIF or PDBQT file, and turn it in 3D. Pick cartoon, sticks, spacefill or a surface, colour by chain or B-factor, find the ligands and read the method and resolution. It is free and runs in your browser.

Quick answer: Press Crambin example (1CRN). It loads a 46-residue plant protein (327 atoms, chain A) as a cartoon with 2 helices and a small β-sheet. Type 1HSG and press Load PDB ID to see HIV-1 protease with the drug indinavir (MK1) as a magenta ligand.

PDB ID (fetched from RCSB PDB)

Try:

Open file (.pdb, .cif, .pdbqt)

Or paste PDB / mmCIF / PDBQT text

Load a structure to start.

The 3D model appears here. Drag to rotate, scroll or pinch to zoom, double-click to reset.

Style Colour by

Highlight ligands (magenta carbons) Show water Show hydrogens (if present) Molecular surface Spin

Hover to see a residue. Click an atom to pin its label.

How to view a PDB file online

Type a PDB ID such as 1HSG and press Load PDB ID, press Open file, or paste the text and press View structure.
Pick a Style: cartoon, ball and stick, sticks, spacefill or lines.
Pick Colour by: chain, element, residue type, secondary structure, rainbow, hydrophobicity or B-factor.
Tick Show water, Hydrogens or Molecular surface as needed. Press Zoom next to a ligand in the table to see the residues within 4 Å.
Hover for residue names, click to pin labels, then press Save PNG.

What the viewer reads

Format	What is used
PDB (.pdb, .ent)	ATOM and HETATM records of the first model (or the model you pick), HELIX and SHEET records, CONECT bonds, HEADER, TITLE, EXPDTA, COMPND, SOURCE and REMARK 2 (resolution). Alternate locations: the first one in each residue is shown.
mmCIF (.cif)	The `_atom_site` table (author chain and residue numbers), `_struct_conf` and `_struct_sheet_range` for helices and sheets, `_exptl.method`, `_refine.ls_d_res_high` or the EM resolution, `_struct.title` and the polymer entity names.
PDBQT (AutoDock, Vina)	Coordinates with AutoDock atom types turned back into elements (A and C → C, OA → O, NA and NS → N, SA → S, HD → H). Each docking pose is a model; the Vina score from `REMARK VINA RESULT` is shown in the model list.

How things are drawn

The viewer uses MolDraw's own WebGL2 renderer. Atoms and bonds are drawn as true spheres and cylinders. The cartoon follows the backbone (Cα for proteins, phosphorus for nucleic acids): helices as wide ribbons, strands as arrows, loops as tubes. Secondary structure comes from the HELIX/SHEET records; if a file has none, it is estimated from backbone hydrogen bonds (a simplified DSSP). The molecular surface is the solvent-excluded surface for a 1.4 Å probe, computed on a grid in your browser.

Bonds come from CONECT records and from distances (covalent radii). Ligands are HETATM groups that are not water and not part of the chain; single metal atoms or halide ions are listed as ions. The B-factor colours run blue (lowest in the file) through white to red (highest).

Limitations

Bond orders are not shown; ligands are drawn with single bonds only.
Only one alternate location per residue is shown, and anisotropic B-factors are ignored.
The surface is for display: it is computed on a grid (0.6–0.9 Å spacing), and very large structures may take several seconds or be slow on phones.
Chain IDs longer than one character in mmCIF files are renamed to single letters for display, and the tool shows the mapping.
Biological assemblies are not built; you see the asymmetric unit (or the model) as stored in the file.
Files you open or paste stay in your browser. A PDB ID is fetched from files.rcsb.org.

Preparing a protein for docking? Clean the PDB, convert it to PDBQT and size the Vina box with the related tools below.

Open the PDB cleaner

Frequently asked questions

How do I open a PDB file online?

Press Open file and choose a .pdb, .ent, .cif (mmCIF) or .pdbqt file, or type a PDB ID such as 1HSG and press Load PDB ID. The file is read in your browser and shown in 3D as a cartoon with ligands as magenta ball-and-stick models. Files you open are not uploaded.

Can it open mmCIF and PDBQT files?

Yes. mmCIF files are read from the _atom_site table, with helices and sheets from _struct_conf and _struct_sheet_range. PDBQT files from AutoDock or Vina are read with their AutoDock atom types turned back into elements (OA to O, NA to N, A to C, HD to H); docking poses appear as models you can switch between, with the Vina score.

Which display styles are available?

Cartoon (helices, sheets and loops), ball and stick, sticks, spacefill (van der Waals spheres), lines and a molecular (solvent-excluded) surface. Colours: chain, element, residue type, secondary structure, rainbow from N- to C-terminus, hydrophobicity and B-factor.

Where do the resolution and method come from?

From the file header: EXPDTA and REMARK 2 in PDB files, _exptl.method and _refine.ls_d_res_high (or the EM reconstruction resolution) in mmCIF files. If the file has no header, the viewer says so instead of guessing.

Why does a large structure not load from its PDB ID?

Very large entries (for example ribosomes) have no .pdb file at the RCSB; the viewer then loads the mmCIF file instead. Structures with hundreds of thousands of atoms can still be slow on phones, so start with the cartoon style.

Last updated: October 30, 2026