A stereoscopic viewing tool by modified OpenRasmol

This web page is written by Masayuki Irisa, Jun.(2005)

RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. OpenRasmol, open source versions of RasMol, is widely known molecular graphics software, which has been used by researchers in scientific field and teachers in education.

We have modified OpenRasmol version 2.7.1 to apply stereoscopic viewing with an eye-ware. One of the famous eye-ware for active stereo is CrystalEyes, which is LCD shutter glasses. Our modified OpenRasmol can be used within a framework of virtual reality system. We keep benefits of OpenRasmol including fast software rendering in OpenRasmol. This web page is made to distribute our modification in open source codes following RASLIC, which is a license on OpenRasmol.

It is our pleasure to enjoy our modified OpenRasmol for stereoscopic viewing of molecules, especially large assemblies of proteins. You can use our modified OpenRasol as well as other 3-D molecular graphics programs on quad buffer stereo mode in OpenGL with a eye-ware. We think a system cosisting of the modified OpenRasmol and a Large screen is also usefull for research and education.

Authors of this modification for stereoscopic viewing:
Satoru Gondo, Yuko Fujishima, and Masayuki Irisa*

*corresponding author
E-mail: irisa@bio.kyutech.ac.jp
Department of Bioscience and Bioinformatics
Faculty of Computer Science and Systems Engineering
Kyushu Institute of Technology
JAPAN

Acknowledgement

This work was supported partly from Grants-in-Aid for Scientific Research on Priority Areas (no.16041234) and Scientific Research (C) (no. 14540473) and Exploratory Research (no.15650052) from the Ministry of Education, Culture, Sports, Science and Technology of Japan. We thank T. Yasunaga, K. Kakizaki, and K. Noma for stimulating discussions and helpful suggestions.
We also thank Virtual Reality Project in faculty of Computer Science and Systems Engineering.

*NOTICE:
OpenRasmol 2.7.1 is a stable version but not brand-new version. Visit OpenRasmol web page to know details on versions including the versoin 2.7.1.

Formal web site of OpenRasmol is OpenRasmol Web page, where licenses on this software are explained.

References of OpenRasmol are the following papers.

Roger Sayle and E. James Milner-White. "RasMol: Biomolecular graphics for all", Trends in Biochemical Sciences (TIBS), September 1995, Vol. 20, No. 9, p. 374.

Herbert J. Bernstein, "Recent changes to RasMol, recombining the variants, Trends in Biochemical Sciences (TIBS), September 2000, Vol. 25, No. 9, pp. 453-455.

RASLIC

RASLIC is documented as the followings,
----------------------------------------------

 RasMol License

Even though the authors of the various documents and software found here
have made a good faith effort to ensure that the documents are correct and
that the software performs according to its documentation, and we would
greatly appreciate hearing of any problems you may encounter, the programs
and documents any files created by the programs are provided **AS IS**
without any warranty as to correctness, merchantability or fitness for any
particular or general use.

THE RESPONSIBILITY FOR ANY ADVERSE CONSEQUENCES FROM THE USE OF PROGRAMS OR
DOCUMENTS OR ANY FILE OR FILES CREATED BY USE OF THE PROGRAMS OR DOCUMENTS
LIES SOLELY WITH THE USERS OF THE PROGRAMS OR DOCUMENTS OR FILE OR FILES AND
NOT WITH AUTHORS OF THE PROGRAMS OR DOCUMENTS.

Subject to your acceptance of the conditions stated above, and your respect
for the terms and conditions stated in the notices in NOTICE, if you are not
going to make any modifications or create derived works, you are given
permission to freely copy and distribute this package, provided you do the
following:

   * 1. Either include the complete documentation, especially the file
     NOTICE, with what you distribute or provide a clear indication where
     people can get a copy of the documentation; and
   * 2. Give credit where credit is due citing the version and original
     authors properly; and
   * 3. Do not give anyone the impression that the original authors are
     providing a warranty of any kind.

In addition, you may also modify this package and create derived works
provided you do the following:

   * 4. Explain in your documentation how what you did differs from this
     version of RasMol; and
   * 5. Make your modified source code available.
------------------------------------------------------------------------

Video files on rendering speed of our modified OpenRasmol in stereoscopic mode

Sample: A 16-mer actin filament consisting of idential single actin molecules of 400 residues
A stop watch can be seen besides the display.
ATI RADEON 8500, 1024*768, full screen.

OpenRasmol:

* Space filling model with stereoscopic mode, RADEON 8500
OpenRasmol, space filling, stereo
OpenRasmol, space filling, no stereo (close up)
* Space filling model with non-sterreoscopic mode, RADEON 8500
OpenRasmol, space filling, no stereo
OpenRasmol, space filling, no stereo (close up)

VMD:
* Space filling model with stereoscopic mode, RADEON 8500
VMD, space filling, stereo
VMD, space filling, stereo (close up)

* Space filling model with non-stereoscopic mode, RADEON 8500
VMD, space filling, no stereo
VMD, space filling, no stereo (close up)

* VMD with non-stereoscopic mode, brand-new 3D board, Nvidia Quadra FX (PCI)
VMD, space filling, no stereo (brand-new 3D board)
VMD, space filling, no stereo (close up, brand-new 3D board)

Downloads

How to use:
Before running our modified OpenRasmol, machines are set to use quad buffer stereo mode in OpenGL.
Most of computers have optional products of 3-D graphic accelerater which enables quad buffer stereo mode in OpenGL.
Just use as native version of OpenRasmol. The menu, "Options"->"Stereo", is replaced from stereoscopic viewing mode form with bare eyes to with an eye-ware (active stereo). In the native OpenRasmol, vertically divided two images are shown. But, in the modified OpenRasmol, one image is shown in quad buffer stereo mode.

Source codes which we have modified:

Native source codes of OpenRasmol version 2.7.1 are distributed in OpenRasmol web page.
source codes of OpenRasmol version 2.7.1

Stereoscopic viewing patch version 0.9.1 for linux machine.
RasMol_2.7.1_stereoscopic_0.9.1.diff

In this period, our modified OpenRasmol is distributed without a function of 3-D pointer(See NOTICE).


How to apply this patch:
ls RasMol_2.7.1_stereoscopic_0.9.1.diff   <------ check for the existence of the patch
gunzip RasMol_2.7.1.tar.gz
tar xvf RasMol_2.7.1.tar              <------ extract the native version
cd RasMol_2.7.1
patch -p1 < ../RasMol_2.7.1_stereoscopic_0.9.1.diff
cd src
xmkmf
make

Binary codes for convenience:

Linux(Vine Linux 2.6, which corresponds to RedHat ***) with quad buffer stereo mode in OpenGL.
rasmol_linux



SUN sparc workstaion with quad buffer stereo mode in OpenGL.
(elite3D or higher SUN 3-D graphics board) 
rasmol_solaris_sparc


SGI workstation with quad buffer stereo mode in OpenGL.
(Octane)
Now, we are checking binary codes on SGI Octane. Please wait.

*NOTICE:
Full color environment required.
Some parts of source codes which we have added for a 3-D pointer using ISOTRACK is under preparation.
Because, we are checking licenses on source codes which are borrowed from sample codes of ISOTRACK.
ISOTRACK is a commercial virtual reality product sensing 3-D realtime position and orientation.