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Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes - PubMed

Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes

Stefan Birmanns et al. J Struct Biol. 2011 Mar.

Abstract

We describe an integrated software system called Sculptor that combines visualization capabilities with molecular modeling algorithms for the analysis of multi-scale data sets. Sculptor features extensive special purpose visualization techniques that are based on modern GPU programming and are capable of representing complex molecular assemblies in real-time. The integration of graphics and modeling offers several advantages. The user interface not only eases the usually steep learning curve of pure algorithmic techniques, but it also permits instant analysis and post-processing of results, as well as the integration of results from external software. Here, we implemented an interactive peak-selection strategy that enables the user to explore a preliminary score landscape generated by the colors tool of Situs. The interactive placement of components, one at a time, is advantageous for low-resolution or ambiguously shaped maps, which are sometimes difficult to interpret by the fully automatic peak selection of colors. For the subsequent refinement of the preliminary models resulting from both interactive and automatic peak selection, we have implemented a novel simultaneous multi-body docking in Sculptor and Situs that softly enforces shape complementarities between components using the normalization of the cross-correlation coefficient. The proposed techniques are freely available in Situs version 2.6 and Sculptor version 2.0.

Copyright © 2010 Elsevier Inc. All rights reserved.

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Figures

Figure 1
Figure 1

Overview of the proposed “Interactive Global Docking” workflow. The multi-resolution data is first analyzed using an exhaustive search approach in Situs (Wriggers, 2010): The program colores exports the preliminary score landscape (translation function) as a 3D map of maximum CC values. The rotations corresponding to each voxel, determined by an exhaustive search of three Euler angles with user-selected rotational granularity, are exported as a 3D map of indices into a rotation table (green and red boxes). In Sculptor, the interactive peak search based on the preliminary scores yields a preliminary model of the entire complex, which is then further optimized using the new multi-body refinement procedure.

Figure 2
Figure 2

Screenshot of the graphical user interface of Sculptor. The software is organized around the main 3D rendering panel, and minor panels are grouped into non-overlapping frames. The upper section of the left panel shows a list of the loaded data files along with their type, and their visibility and mobility status (the lower half of the panel changes its content based on the selected document). In the screenshot, the volumetric map is selected and the direct volume rendering tab is shown. The user can freely define the transfer function (mapping of material properties to intensities) based on the histogram of the map. The bottom right section shows the log panel, where the program communicates the status and outcome of commands and algorithms.

Figure 3
Figure 3

Software architecture of Sculptor. The main application program comprises only a thin software layer on top of a C++ class library, which is subdivided into modules. Low-level modules like “System,” which connects the library with the different operating systems, form the basis for higher-level modules. The “Library for Input devices in Virtual Environments” (L.I.V.E.) provides routines to dynamically load device drivers for special input devices like the SensAble 6DOF or Novint Falcon force feedback controllers. “Core” implements a general purpose 3D scenegraph architecture, which is extended by high-level modules that provide nodes to visualize specific data types. Sculptor uses the visualization nodes for atomic models and volumetric maps, although additional high-level modules exist for other applications.

Figure 4
Figure 4

Direct volume rendering permits the visualization of soft boundaries in volumetric maps. Shown here is an interactive visualization of the DegP protease-chaperone in Sculptor (EMDB code: 1504).

Figure 5
Figure 5

Different stages of interactive peak search shown as direct screen captures from Sculptor: Docking of subunits into the 14 Å cryo-EM map of the actomyosin complex (Holmes et al., 2003). (A)–(B) The user translates the G-actin monomer as desired inside the map, while the optimal rotation at each position is updated in real time. The color of the central sphere and the numeric value reflect the (normalized) CC value. (C)–(E) Two G-actin monomers are docked (yellow ribbons) and fixed, while a third G-actin monomer is translated inside the map. (E)–(F) Contacts are shown between the mobile G-actin monomer and the fixed monomers (favorable contacts are displayed as green spheres and steric clashes in red). (F) The myosin S1 fragment docked inside the map of the complex.

Figure 6
Figure 6

The actomyosin complex: Multi-body refinement of 12 G-actin monomers / 12 myosin S1 inside the 14 Å-resolution map

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