Willy Wriggers and Stefan Birmanns. Using Situs for Flexible and Rigid-Body Fitting of Multi-Resolution Single Molecule Data. Journal of Structural Biology. Vol. 133, pp. 193-202.
We describe here a set of multi-resolution visualization and docking procedures that we refer to as the Situs package. The package was developed to provide an efficient and robust method for the fitting of atomic structures into low-resolution data. The current release was optimized specifically for the visualization and docking of single molecules. A novel 3D graphics viewer, volslice3d, was developed for the package to provide an immersive virtual reality environment for measuring and rendering volumetric data sets. The precision of single-molecule, rigid-body docking was tested on simulated (noise-free) low-resolution density maps. For spatial resolutions near 20 A typically arising in electron microscopy image reconstructions, a docking precision on the order of an Angstrom can be achieved. The shape-matching score captured the correct solutions in all ten trial cases and was sufficiently stringent to yield unique matches in eight systems. Novel routines were developed for the flexible docking of atomic structures whose shape deviates from the corresponding low-resolution shape. Test calculations on isoforms of actin and lactoferrin demonstrate that the flexible docking faithfully reproduces conformational differences with a precision < 2 A if atomic structures are locally conserved.
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