Visualize Options



NGL is a fast & interactive web-based tool for 3D visualization of large structures. For X-ray structures, crystallographic unit cells can be displayed, as well as "supercells" comprising a set of adjacent unit cells.


Jsmol and Jmol

JSmol, the JavaScript version of Jmol offers several options for display and analysis. Launch the viewer from any entry's Structure Summary page or by entering an ID below.  The Jmol Applet remains available from the 3D View page, and will continue to work in most browsers.  Learn more about Jsmol/Jmol.


Simple Viewer and Protein Workshop

RCSB PDB created these Java Web Start applications for 3D visualization. Launch the specific viewer from each entry's Structure Summary.

Launch each viewer for Hemoglobin (4HHB) below.

Simple Viewer can rotate a structure, zoom in and out, and then save the view of the biological unit as an image file.

Protein Workshop can quickly and easily select structural elements to change the coloring, labeling, and representation style to highlight conformation type, hydrophobicity, residue type, and more.


Ligand Explorer

This Java Web Start program from RCSB PDB visualizes macromolecular-ligand interactions in 3D.

Ligand Explorer has options to turn on the display of interactions including hydrogen bonds, hydrophobic contacts, water mediated hydrogen bonds, and metal interactions.

It can be launched from an entry's Structure Summary.



PoseView images are 2D diagrams that show a ligand and interacting residues.

Black dashed lines indicate hydrogen bonds, salt bridges, and metal interactions. Green solid line show hydrophobic interactions and green dashed lines show π-π and π-cation interactions.

Access PoseView images in the Ligand Chemical Component section on an entry's Structure Summary.

Learn more about PoseView.


Protein Feature View

Provides a graphical summary of a full-length protein sequence from UniProt and how it corresponds to PDB entries. It also loads annotations from external databases (such as Pfam) and homology models information from the Protein Model Portal. Annotations visualizing predicted regions of protein disorder and hydrophobic regions are displayed.

Learn more about Protein Feature View.

Examples: Breast Cancer Type 1 Protein, Gag-Pol Polyprotein, and Hemoglobin Alpha (shown image).

This feature is available from the Molecular Description widget on Structure Summary pages and by entering a UniProt ID below.


Human Gene View

Illustrates the correspondences between the human genome and 3D structure. All human genes have been mapped to representative PDB structure protein chains (selected from sequence clusters at 40% sequence identity) to show which regions of a gene are available in PDB coordinates.

Learn more about Gene View.

Examples: Breast Cancer 1 (early onset) and Hemoglobin, Alpha 1 (shown image).

This feature is available from the Molecular Description widget on Structure Summary pages and by entering an HGNC Human Gene Symbol below (examples).


Pathway View

Explore metabolic pathways maps that identify pathway components with PDB structures and homology models.

Maps can be accessed from Structure Summary pages (see example 3MOS), Protein View (see example P29401), and the main Pathway View page.