UCSF Chimera Extensions

UCSF Chimera [1] is a widely used software for the visualization and modeling of protein 3D structures. We developed two extensions which support the analysis of protein variants and protein engineering.

The first extension offers an interface to our online service MAESTRO [2], a versatile tool for the prediction of stability changes upon point mutations. The extension provides access to the most popular application scenarios.

The second extension performs multiple structure alignments (MStAs) by utilizing our web service PIRATES [3]. PIRATES is a meta server for MStAs, which currently provides access to eight widely used alignment methods. In addition, the service computes a consensus alignment based on their results.

Both extensions are written in Python and communicate with our RESTful web service called BioDApps [4]. All components are freely available for academic research and do not have any dependencies other than a UCSF Chimera (version 11.1 or later) installation and an internet connection.


The extensions are free for non-commercial use. By using this software, you accept the terms of the License Agreement. Please do not hesitate to contact us in the case of any questions.

Version 0.8 beta


Unpack the zip file with your favorite packing tool and copy its content into the “share” directory of your UCSF Chimera installation. Open up Chimera and launch Tools> BioDApps> MAESTRO or Tools> BioDApps> PIRATES, respectively.

Missing Features and Known Issues

A user manual is not yet available but will be provided soon. Please do not hesitate to contact us in the case of any questions.


[1] UCSF Chimera – a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12. PMID: 15264254

[2] MAESTRO – multi agent stability prediction upon point mutations. Laimer J, Hofer H, Fritz M, Wegenkittl S, Lackner P. BMC Bioinformatics 2015, 16:116 doi:10.1186/s12859-015-0548-6. PMID: 25885774

[3] PIRATES – Protein Structure Alignment Meta Server. Doblmann J, Haunschmid V, Holzmann H, Stütz C, Laimer J, Lackner P. Poster, ÖGMBT Annual Meeting 2012. link.

[4] BioDApps – Distributed Bioinformatics Applications. Bernwinkler T, Hiebl-Flach J, Katzenschlager J, Köberl D, Lengauer D, Nagl L, Schubert S, Laimer J, Lackner P. Poster, ÖGMBT Annual Meeting 214. link.