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Stereoscopic viewing system for proteins using OpenRasmol: a tool for displaying a filament of proteins

View Article: PubMed Central - PubMed

ABSTRACT

We have made a stereoscopic viewing system for a large assembly of proteins using OpenRasmol. The stable version 2.7.1 of OpenRasmol is modified for the system, which uses an eye-ware instead of trained bare-eyes. Software rendering and other benefits in OpenRasmol are reserved. A 3-D graphic board is used just for the active stereo method, not for the acceleration of rendering. Our modification is simple one. In the results, an actin filament of 16-mers, where one actin monomer has about 400 residues, in space filling model can be rendered in stereoscopic viewing mode and can be made one turn within 10 seconds as quick as non-stereoscopic mode. Other 3-D molecular graphics programs with 3-D accelerator boards cannot render such a large assembly of molecules in stereoscopic usage mode as quickly as the modified OpenRasmol. An attractive application of our system is stereoscopic viewing with a large 200 inch screen in passive stereo method. Simultaneous usage is available for more than 100 persons with inexpensive eye-wares. The large screen allows us to investigate an interior of a groove in an actin filament in detail. Our modified OpenRasmol is distributed following the license, RASLIC, as an open source code at our web site (www.irisa-lab.bio.kyutech.ac.jp/openrasmol), where video files showing rendering speeds of our modified OpenRasmol are also available.

No MeSH data available.


Related in: MedlinePlus

Images of an actin filament using space filling model in modified OpenRasmol. A) whole image of the filament, More than 70000 spheres are rendered in this figure. Each heavy atom is colored gray (carbon), red (oxygen), blue (nitrogen), or yellow (sulfur), respectively. B) Image zoomed about 5 times from the previous one. The filament consists of 16 monomers each of which has about 400 residues. Each molecule is colored in gradation from blue to red along the main chain of the protein. Display resolution is XVGA. For convenience, figures are monocular mode, but stereoscopic viewing mode is enabled in the system of modified OpenRasmol.
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f2-3_57: Images of an actin filament using space filling model in modified OpenRasmol. A) whole image of the filament, More than 70000 spheres are rendered in this figure. Each heavy atom is colored gray (carbon), red (oxygen), blue (nitrogen), or yellow (sulfur), respectively. B) Image zoomed about 5 times from the previous one. The filament consists of 16 monomers each of which has about 400 residues. Each molecule is colored in gradation from blue to red along the main chain of the protein. Display resolution is XVGA. For convenience, figures are monocular mode, but stereoscopic viewing mode is enabled in the system of modified OpenRasmol.

Mentions: We checked our system for assembled proteins. An actin filament8 is used as an example which is a double helix consisted of arranged actin monomers of about 400 residues in each monomer (Figure 2). The term “polymerization” is used in the formation of an actin filament. But in physicochemical sense, actin monomers are associated into an actin filament. There is no covalent bond between actin molecules in the actin filament. Many studies on actin molecules have been reported8 because actin has wide variety of biological functions in a cell as a motor protein. It is important to investigate the structure of actin filament where ATP, phalloidin and other small molecules are attached depending on biological conditions. Experiments with X-ray diffraction or electron microscope require detailed stereoscopic visualization of molecules in a large filament structure. In the application of computer graphics, size of an actin molecule is large to render in space filling model because a sphere representing an atom needs a lot of polygons to be displayed with a smooth surface. An actin filament consisting of 16 molecules is used as a sample to check modified OpenRasmol for stereoscopic viewing. Speed of stereoscopic rendering using the modified OpenRasmol is enough for large proteins and assembled proteins like actin filaments.


Stereoscopic viewing system for proteins using OpenRasmol: a tool for displaying a filament of proteins
Images of an actin filament using space filling model in modified OpenRasmol. A) whole image of the filament, More than 70000 spheres are rendered in this figure. Each heavy atom is colored gray (carbon), red (oxygen), blue (nitrogen), or yellow (sulfur), respectively. B) Image zoomed about 5 times from the previous one. The filament consists of 16 monomers each of which has about 400 residues. Each molecule is colored in gradation from blue to red along the main chain of the protein. Display resolution is XVGA. For convenience, figures are monocular mode, but stereoscopic viewing mode is enabled in the system of modified OpenRasmol.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036655&req=5

f2-3_57: Images of an actin filament using space filling model in modified OpenRasmol. A) whole image of the filament, More than 70000 spheres are rendered in this figure. Each heavy atom is colored gray (carbon), red (oxygen), blue (nitrogen), or yellow (sulfur), respectively. B) Image zoomed about 5 times from the previous one. The filament consists of 16 monomers each of which has about 400 residues. Each molecule is colored in gradation from blue to red along the main chain of the protein. Display resolution is XVGA. For convenience, figures are monocular mode, but stereoscopic viewing mode is enabled in the system of modified OpenRasmol.
Mentions: We checked our system for assembled proteins. An actin filament8 is used as an example which is a double helix consisted of arranged actin monomers of about 400 residues in each monomer (Figure 2). The term “polymerization” is used in the formation of an actin filament. But in physicochemical sense, actin monomers are associated into an actin filament. There is no covalent bond between actin molecules in the actin filament. Many studies on actin molecules have been reported8 because actin has wide variety of biological functions in a cell as a motor protein. It is important to investigate the structure of actin filament where ATP, phalloidin and other small molecules are attached depending on biological conditions. Experiments with X-ray diffraction or electron microscope require detailed stereoscopic visualization of molecules in a large filament structure. In the application of computer graphics, size of an actin molecule is large to render in space filling model because a sphere representing an atom needs a lot of polygons to be displayed with a smooth surface. An actin filament consisting of 16 molecules is used as a sample to check modified OpenRasmol for stereoscopic viewing. Speed of stereoscopic rendering using the modified OpenRasmol is enough for large proteins and assembled proteins like actin filaments.

View Article: PubMed Central - PubMed

ABSTRACT

We have made a stereoscopic viewing system for a large assembly of proteins using OpenRasmol. The stable version 2.7.1 of OpenRasmol is modified for the system, which uses an eye-ware instead of trained bare-eyes. Software rendering and other benefits in OpenRasmol are reserved. A 3-D graphic board is used just for the active stereo method, not for the acceleration of rendering. Our modification is simple one. In the results, an actin filament of 16-mers, where one actin monomer has about 400 residues, in space filling model can be rendered in stereoscopic viewing mode and can be made one turn within 10 seconds as quick as non-stereoscopic mode. Other 3-D molecular graphics programs with 3-D accelerator boards cannot render such a large assembly of molecules in stereoscopic usage mode as quickly as the modified OpenRasmol. An attractive application of our system is stereoscopic viewing with a large 200 inch screen in passive stereo method. Simultaneous usage is available for more than 100 persons with inexpensive eye-wares. The large screen allows us to investigate an interior of a groove in an actin filament in detail. Our modified OpenRasmol is distributed following the license, RASLIC, as an open source code at our web site (www.irisa-lab.bio.kyutech.ac.jp/openrasmol), where video files showing rendering speeds of our modified OpenRasmol are also available.

No MeSH data available.


Related in: MedlinePlus