About Sculptor

Sculptor is an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures. We are developing Sculptor as a GUI-based extension of the Situs docking programs, to allow an interactive exploration and analysis of volumetric maps. Sculptor combines 3D rendering with advanced mathematical concepts like clustering techniques and pattern matching algorithms to permit an almost instantaneous fitting of the high-resolution structures and to facilitate typical post-processing work like map editing or resolution adjustment.

Recent releases have added routines to efficiently model conformational differences, to interactively carry out the peak-selection for exhaustive search tools, and have added accelerated visualization techniques using programmable-GPUs.

 







 

Interested in joining our team and helping to develop Sculptor? We have several open positions. Read More.

 
Sculptor Version 1.2.1

 

 

A new bugfix release, Sculptor Version 1.2.1, is available. Several small bugs were fixed and some smaller new features introduced, including the following:

1. Cg updated to the latest version 2.2 / October 2009 (the old version in the previous package caused problems on newer Linux distributions).
2. Changing the voxelwidth does not trigger Sculptor to regard the document as being altered. Spider files do not store the information about the voxelwidth in the file, so the user has to input this information in Sculptor manually. The previous versions of Sculptor have then forced the user to save the file, as the program regarded the volume as being altered.
3. Various small bugfixes around the volume-rendering. Under some conditions the direct volume rendering could become out-of-scale. The rendering of the cross-sections was improved.
4. The overall scaling of the scene is now stored in the state files.

 

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Sculptor Version 1.2

A new Sculptor release, version 1.2, is available. This release includes ¨interactive global docking¨ as a major new feature, but also adds programmable-GPU accelerated rendering of atomic models, other smaller improvements and bug fixes.


Interactive Global Docking (IGD) is a novel technique that permits an interactive peak search in score-maps generated from exhaustive docking tools like Situs/Colores - please see also the new Situs release 2.5, which has support for IGD built into Colores. In experimental volumetric maps with a heterogeneous density distribution, or significant areas that are not accounted for by the atomic model, multi-resolution docking can be problematic. The correct solution is then difficult for the automatic algorithms to detect, as the docking contrast - the numerical difference of scores of false and true positive solutions - can become very small. An interactive screening of the scoring landscape allows the user to select carefully the potential solutions, which then can be further optimized using an off-lattice refinement technique. Please click on the image below to see a video with the interactive global docking in action:

 

 

Programmable-GPU accelerated rendering and shading of tube, cartoon and van-der-Waals representations. The new code is optimized especially for low-end machines with inexpensive graphics cards (for example netbooks with integrated Intel GMA950 graphics chips, like the Asus EEE PC) and does not only lead to a higher-quality representation, but at the same time also achieves a significantly higher performance. It also permits the investigation of large pleiomorphic systems, especially in combination with the efficient flexible fitting technique which was introduced in Sculptor 1.1 / Situs 2.4.

 

 

 

 

Speed improvements and code-cleanup in the areas of the cross-correlation coefficient calculation, loading and saving of volumetric maps, display of the coordinate system and clipping planes. Rendering problems under Microsoft Vista were also fixed.

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Participation

Research directly related to Sculptor was / will be presented at the following conferences:

 

Invited talks:

Microscopy and Microanalysis 2010

August 1-5, Portland, OR

 

 

3D Electron Microscopy of Macromolecular Assemblies
Teresa Ruiz, Michael Radermacher, and Stefan Birmanns

Slides

 

Parallel Genetic Algorithm with Biased Initial Population for the Simultaneous Hybrid Modeling of Molecular Assemblies

Mirabela Rusu, and Stefan Birmanns

 


Poster presentation:

Biophysical Society Meeting 2010
San Francisco, California, February 20 - 24, 2010
Integrative Multi-Resolution Modeling of Pleiomorphic Biomolecular Systems
Mirabela Rusu and Stefan Birmanns

 

 


Invited talk:

4th International UVM Practical Course on Three-dimensional Cryo Electron Microscopy of Single Particles
University of Vermont, Burlington, VT, August 2 - 9, 2009
http://physioweb.med.uvm.edu/Cryo_Practical

 

 


Poster presentation:

Biophysical Society Meeting 2009
Boston, Massachusetts, February 28 - March 4, 2009
Integrative Multi-Resolution Modeling of Pleiomorphic Biomolecular Systems
Mirabela Rusu and Stefan Birmanns

Interactive Visualization of Protein Dynamics in Ribbon Mode
Manuel Wahle and Stefan Birmanns

Incorporating  Exhaustive Search and Steric Effects into Interactive Multi-Resolution Modeling
Jochen Heyd and Stefan Birmanns


Invited talk:

University of Vermont, Burlington. Hosts: Teresa Ruiz and Michael Radermacher
Sculptor: A software package for interactive and algorithmic multi-resolution modeling.
Stefan Birmanns
Burlington, VT, December 8th, 2008


Invited talk:

Microscopy and Microanalysis 2008
Beyond the Black-Box: Multi-Modal Hybrid Modeling of Biomolecular Assemblies
Jochen Heyd and Stefan Birmanns
Albuquerque, New Mexico,
August 3-7, 2008.

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