Limits...
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.


Schematic illustration of data flow of our modified OpenRasmol: hardware and software parts are connected to enable both quick rendering and usages of 3-D devices in time. The instantaneous geometry is calculated in the software to find the corresponding 3-D object that 3-D pointer is pointing. Because the geometry data contained in 3-D graphics board cannot be extracted from the board. The shaded part is added to OpenRasmol for modifications in this work.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC5036655&req=5

f1-3_57: Schematic illustration of data flow of our modified OpenRasmol: hardware and software parts are connected to enable both quick rendering and usages of 3-D devices in time. The instantaneous geometry is calculated in the software to find the corresponding 3-D object that 3-D pointer is pointing. Because the geometry data contained in 3-D graphics board cannot be extracted from the board. The shaded part is added to OpenRasmol for modifications in this work.

Mentions: Our modifications have three new features. First, both software and hardware rendering is used (Figure 1). Molecules are rendered in software rendering. Software Z-buffer2 in Rasmol has been used for this purpose. Second, 3-D pointer has been made with 3-D input devices. Third, finding function of matched position of 3-D pointer position with an atom in virtual reality space utilizes Rasmol Z-buffer, which reduces computational cost of geometrical calculation of interactive operation, e.g. rotation. Hardware rendering usually does not allow direct usage of calculated geometrical positions of 3-D objects in the graphics memory on-board. To identify the 3-D object that a 3-D pointer points, programmers are forced to make the function that search the painted 3-D object from geometry calculated in the application in spite of the existence of the same calculated geometry contained in the graphics board.


Stereoscopic viewing system for proteins using OpenRasmol: a tool for displaying a filament of proteins
Schematic illustration of data flow of our modified OpenRasmol: hardware and software parts are connected to enable both quick rendering and usages of 3-D devices in time. The instantaneous geometry is calculated in the software to find the corresponding 3-D object that 3-D pointer is pointing. Because the geometry data contained in 3-D graphics board cannot be extracted from the board. The shaded part is added to OpenRasmol for modifications in this work.
© Copyright Policy
Related In: Results  -  Collection

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

f1-3_57: Schematic illustration of data flow of our modified OpenRasmol: hardware and software parts are connected to enable both quick rendering and usages of 3-D devices in time. The instantaneous geometry is calculated in the software to find the corresponding 3-D object that 3-D pointer is pointing. Because the geometry data contained in 3-D graphics board cannot be extracted from the board. The shaded part is added to OpenRasmol for modifications in this work.
Mentions: Our modifications have three new features. First, both software and hardware rendering is used (Figure 1). Molecules are rendered in software rendering. Software Z-buffer2 in Rasmol has been used for this purpose. Second, 3-D pointer has been made with 3-D input devices. Third, finding function of matched position of 3-D pointer position with an atom in virtual reality space utilizes Rasmol Z-buffer, which reduces computational cost of geometrical calculation of interactive operation, e.g. rotation. Hardware rendering usually does not allow direct usage of calculated geometrical positions of 3-D objects in the graphics memory on-board. To identify the 3-D object that a 3-D pointer points, programmers are forced to make the function that search the painted 3-D object from geometry calculated in the application in spite of the existence of the same calculated geometry contained in the graphics board.

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.