Biophysical Reviews

, Volume 2, Issue 1, pp 21-27

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

Using Situs for the integration of multi-resolution structures

  • Willy WriggersAffiliated withDepartment of Physiology and Biophysics, Weill Medical College of Cornell UniversityD.E. Shaw Research Email author 


Situs is a modular and widely used software package for the integration of biophysical data across the spatial resolution scales. It has been developed over the last decade with a focus on bridging the resolution gap between atomic structures, coarse-grained models, and volumetric data from low-resolution biophysical origins, such as electron microscopy, tomography, or small-angle scattering. Structural models can be created and refined with various flexible and rigid body docking strategies. The software consists of multiple, stand-alone programs for the format conversion, analysis, visualization, manipulation, and assembly of 3D data sets. The programs have been ported to numerous platforms in both serial and shared memory parallel architectures and can be combined in various ways for specific modeling applications. The modular design facilitates the updating of individual programs and the development of novel application workflows. This review provides an overview of the Situs package as it exists today with an emphasis on functionality and workflows supported by version 2.5.


Structural models 3D data sets Multi-platform Modeling