UCSF Chimera is a program for the interactive visualization and analysis of molecular structures and related data, including density maps, trajectories, and sequence alignments. It is available free of charge for noncommercial use. Commercial users, please see Chimera commercial licensing.

We encourage Chimera users to try ChimeraX for much better performance with large structures, as well as other major advantages and completely new features in addition to nearly all the capabilities of Chimera (details...).

Chimera is no longer under active development. Chimera development was supported by a grant from the National Institutes of Health (P41-GM103311) that ended in 2018.

Feature Highlight

Multiple Sequence Alignment

Multiple sequence alignment of structure chains in Chimera or realignment of the sequences in an existing alignment can be performed using web services hosted by the UCSF RBVI. The following programs are provided:

• Clustal Omega
• MUSCLE

The result is automatically shown in Multalign Viewer. (Sequences can also be added to an alignment one by one without a web service, but true multiple sequence alignment is often advantageous.) (More features...)

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Gallery Sample

Binding Site Similarity

β-1,4-glycanase (gold, PDB 1exp) and cellobiohydrolase I (cyan, PDB 1cel) have similar glucose-binding sites but different folds. Ribbons were slimmed with Ribbon Style Editor and the title and captions were added with 2D Labels (see image how-to). (More samples...)