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Using Situs for the integration of multi-resolution structures.

Wriggers W - Biophys Rev (2010)

Bottom Line: 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.ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-009-0026-3) contains supplementary material, which is available to authorized users.

View Article: PubMed Central - PubMed

ABSTRACT
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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-009-0026-3) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus

Schematic diagram of SAXS-related routines in Situs 2.5. Visualization and modeling of atomic structures into SAXS bead models are supported through a conversion into 3D volumes representing the beads using the pdb2vol kernel convolution tool. Docking between atomic structures and 3D maps can be achieved through a number of approaches (see text). The data can be prepared further for the visualization using a variety of analysis and editing tools. Optional Gaussian kernel convolution with pdb2vol facilitates the smoothing of bead surfaces for their visualization in the form of density isocontours
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Fig3: Schematic diagram of SAXS-related routines in Situs 2.5. Visualization and modeling of atomic structures into SAXS bead models are supported through a conversion into 3D volumes representing the beads using the pdb2vol kernel convolution tool. Docking between atomic structures and 3D maps can be achieved through a number of approaches (see text). The data can be prepared further for the visualization using a variety of analysis and editing tools. Optional Gaussian kernel convolution with pdb2vol facilitates the smoothing of bead surfaces for their visualization in the form of density isocontours

Mentions: 3D bead models of proteins in solution can be determined from 1D scattering data, in particular from SAXS (Chacón et al. 2000). Wriggers and Chacón (2001a) extended existing Situs tools to provide an atomic interpretation of SAXS-derived shapes. The workflow and the programs that are used to dock an atomic structure into low-resolution SAXS models are shown schematically in Fig. 3. The bead models can be transformed into volumetric maps for subsequent docking using convolution with a hard sphere kernel (pdb2vol tool). The SAXS modeler then has access to all docking strategies supported by Situs, including correlation-based docking (colacor/colores) and point cloud matching (qrange/matchpoint), and even flexible fitting (see below). To test the docking accuracy, we added the pdb2saxs tool to map atomic structures of trial proteins to hexagonal close-packed lattices with variable bead radii. The resulting models served as “simulated” low-resolution data in Wriggers and Chacón (2001a): For >100 beads typically arising in SAXS models, a rigid body docking precision can be achieved of the order of an Angstrom.Fig. 3


Using Situs for the integration of multi-resolution structures.

Wriggers W - Biophys Rev (2010)

Schematic diagram of SAXS-related routines in Situs 2.5. Visualization and modeling of atomic structures into SAXS bead models are supported through a conversion into 3D volumes representing the beads using the pdb2vol kernel convolution tool. Docking between atomic structures and 3D maps can be achieved through a number of approaches (see text). The data can be prepared further for the visualization using a variety of analysis and editing tools. Optional Gaussian kernel convolution with pdb2vol facilitates the smoothing of bead surfaces for their visualization in the form of density isocontours
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2821521&req=5

Fig3: Schematic diagram of SAXS-related routines in Situs 2.5. Visualization and modeling of atomic structures into SAXS bead models are supported through a conversion into 3D volumes representing the beads using the pdb2vol kernel convolution tool. Docking between atomic structures and 3D maps can be achieved through a number of approaches (see text). The data can be prepared further for the visualization using a variety of analysis and editing tools. Optional Gaussian kernel convolution with pdb2vol facilitates the smoothing of bead surfaces for their visualization in the form of density isocontours
Mentions: 3D bead models of proteins in solution can be determined from 1D scattering data, in particular from SAXS (Chacón et al. 2000). Wriggers and Chacón (2001a) extended existing Situs tools to provide an atomic interpretation of SAXS-derived shapes. The workflow and the programs that are used to dock an atomic structure into low-resolution SAXS models are shown schematically in Fig. 3. The bead models can be transformed into volumetric maps for subsequent docking using convolution with a hard sphere kernel (pdb2vol tool). The SAXS modeler then has access to all docking strategies supported by Situs, including correlation-based docking (colacor/colores) and point cloud matching (qrange/matchpoint), and even flexible fitting (see below). To test the docking accuracy, we added the pdb2saxs tool to map atomic structures of trial proteins to hexagonal close-packed lattices with variable bead radii. The resulting models served as “simulated” low-resolution data in Wriggers and Chacón (2001a): For >100 beads typically arising in SAXS models, a rigid body docking precision can be achieved of the order of an Angstrom.Fig. 3

Bottom Line: 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.ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-009-0026-3) contains supplementary material, which is available to authorized users.

View Article: PubMed Central - PubMed

ABSTRACT
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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s12551-009-0026-3) contains supplementary material, which is available to authorized users.

No MeSH data available.


Related in: MedlinePlus