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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 colores-related routines in Situs 2.5. Major Situs components (blue) are classified by their functionality. The main workflow is indicated by brown arrows. The visualization (orange) for the rendering of the models requires a molecular graphics viewer such as VMD (Humphrey et al. 1996), Chimera (Pettersen et al. 2004), or Sculptor (http://sculptor.biomachina.org). Standard volumetric map formats are converted to cubic lattices in Situs format with the map2map utility. Subsequently, the data are inspected and, if necessary, prepared for the fitting using a variety of visualization and analysis tools. Situs docking tools require one volume (target) and one PDB structure (probe). Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa, to allow the docking of maps to maps or structures to structures. The resulting docked complex can be inspected in the graphics program. In addition, if a subset of Euler angles is chosen, these can be inspected (after conversion into PDB format) with the eul2pdb tool.
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Fig1: Schematic diagram of colores-related routines in Situs 2.5. Major Situs components (blue) are classified by their functionality. The main workflow is indicated by brown arrows. The visualization (orange) for the rendering of the models requires a molecular graphics viewer such as VMD (Humphrey et al. 1996), Chimera (Pettersen et al. 2004), or Sculptor (http://sculptor.biomachina.org). Standard volumetric map formats are converted to cubic lattices in Situs format with the map2map utility. Subsequently, the data are inspected and, if necessary, prepared for the fitting using a variety of visualization and analysis tools. Situs docking tools require one volume (target) and one PDB structure (probe). Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa, to allow the docking of maps to maps or structures to structures. The resulting docked complex can be inspected in the graphics program. In addition, if a subset of Euler angles is chosen, these can be inspected (after conversion into PDB format) with the eul2pdb tool.

Mentions: Chacón and Wriggers (2002) introduced colores, a widely used registration tool that takes advantage of Fourier correlation theory to rapidly scan the six translational and rotational degrees of freedom of a probe molecule relative to a (fixed) target density map. X-ray crystallographic fitting methods, based on volumetric cross-correlation or the free R-value, are limited to resolutions <10 Å where densities exhibit internal structure. The major advantage of colores is that it extends the viable resolution range to ∼30 Å by means of a Laplacian operator that emphasizes contour (shape) information in addition to the traditional correlation. Over the years, we have optimized the efficiency and accuracy of colores and ported the tool to shared memory environments that take advantage of today’s multi-core architectures. The series of steps and the programs that are required to use colores for the docking of a probe structure to a target EM map are shown schematically in Fig. 1.Fig. 1


Using Situs for the integration of multi-resolution structures.

Wriggers W - Biophys Rev (2010)

Schematic diagram of colores-related routines in Situs 2.5. Major Situs components (blue) are classified by their functionality. The main workflow is indicated by brown arrows. The visualization (orange) for the rendering of the models requires a molecular graphics viewer such as VMD (Humphrey et al. 1996), Chimera (Pettersen et al. 2004), or Sculptor (http://sculptor.biomachina.org). Standard volumetric map formats are converted to cubic lattices in Situs format with the map2map utility. Subsequently, the data are inspected and, if necessary, prepared for the fitting using a variety of visualization and analysis tools. Situs docking tools require one volume (target) and one PDB structure (probe). Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa, to allow the docking of maps to maps or structures to structures. The resulting docked complex can be inspected in the graphics program. In addition, if a subset of Euler angles is chosen, these can be inspected (after conversion into PDB format) with the eul2pdb tool.
© Copyright Policy
Related In: Results  -  Collection

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

Fig1: Schematic diagram of colores-related routines in Situs 2.5. Major Situs components (blue) are classified by their functionality. The main workflow is indicated by brown arrows. The visualization (orange) for the rendering of the models requires a molecular graphics viewer such as VMD (Humphrey et al. 1996), Chimera (Pettersen et al. 2004), or Sculptor (http://sculptor.biomachina.org). Standard volumetric map formats are converted to cubic lattices in Situs format with the map2map utility. Subsequently, the data are inspected and, if necessary, prepared for the fitting using a variety of visualization and analysis tools. Situs docking tools require one volume (target) and one PDB structure (probe). Atomic coordinates in PDB format can be transformed to low-resolution maps, if necessary, and vice versa, to allow the docking of maps to maps or structures to structures. The resulting docked complex can be inspected in the graphics program. In addition, if a subset of Euler angles is chosen, these can be inspected (after conversion into PDB format) with the eul2pdb tool.
Mentions: Chacón and Wriggers (2002) introduced colores, a widely used registration tool that takes advantage of Fourier correlation theory to rapidly scan the six translational and rotational degrees of freedom of a probe molecule relative to a (fixed) target density map. X-ray crystallographic fitting methods, based on volumetric cross-correlation or the free R-value, are limited to resolutions <10 Å where densities exhibit internal structure. The major advantage of colores is that it extends the viable resolution range to ∼30 Å by means of a Laplacian operator that emphasizes contour (shape) information in addition to the traditional correlation. Over the years, we have optimized the efficiency and accuracy of colores and ported the tool to shared memory environments that take advantage of today’s multi-core architectures. The series of steps and the programs that are required to use colores for the docking of a probe structure to a target EM map are shown schematically in Fig. 1.Fig. 1

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