Help

3-dimensional interactive models    1. Introduction    2. Recommended 3-dimensional viewers    3. Configuring your WWW browser    4. MIME types used by the IMB Jena server    Close window

Helix and bending analysis of nucleic acid double helix structures

1. Introduction

In addition to the static images we also provide 3-dimensional interactive models. These models can be requested in four different formats: RASMOL scripts, CHIME scripts, VRML 2.0, PDB coordinate files. Table 1 shows which viewer programs can be used for each of these script and coordinate files. The viewers are freely available. They can display the 3-dimensional models interactively. The models can be moved, rotated, or zoomed. RASMOL and CHIME also allow to change the rendering of the model. You can modify the colors of selected parts of the model for example, or even make them invisible. RASMOL and CHIME also offer a stereo display mode.

2. Recommended 3-dimensional viewers

The RASMOL and CHIME scripts are identical, only their MIME types are different. On a WINDOWS PC or MAC you may prefer the CHIME plug-in because it is either already installed or otherwise more easy to install. The appearance of the models is identical with RASMOL and CHIME. The PDB file of a structure offers a much less informative view, because you have to do coloring and rendering by yourself. The PDB files are mainly intended for users who want to get a local copy of the structure for off-line use with other molecular modeling software.

We have tried to make the appearance of the models consistent in all 3-dimensional models and in the GIF images. Coloring, rendering, and the labels are the same in all models. Nevertheless, there is a fundamental difference with the VRML 2.0 models. RASMOL and CHIME present the models in a viewing window with perpendicular and linearly scaled coordinate axes, whereas the VRML 2.0 models are presented in the examiner view. This is a kind of fish-eye perspective, where distant parts of the model are much smaller than parts which are close to the position of the visitor of the VRML scene.

The examiner view is inadequate to explore the bending of a nucleic acid double helix. Bends of the helical axis are none-linearly distorted in this view. Therefore, using the VRML 2.0 models is not recommended. The reason for providing the VRML views is that currently most computers have already installed a VRML plug-in. An occasional visitor of this site may get a first impression of the shape of a nucleic acid double helix from the VRML 2.0 model. But if you are seriously interested in biomolecular structures, you should install either RASMOL or CHIME.

A further advantage of RASMOL and CHIME is that you can change the coloring and rendering of the structures. In this way you may highlight some details which are difficult to see in the standard views. Furthermore, side-by-side stereo representations can be generated with these viewers. You can view these stereo images either with some inexpensive mirror glasses, or (with a little training) simply by crossing your eyes. Stereo 3-dimensional models are by far the most informative way to look for biomolecular structures.

3. Configuring your WWW browser

If you want to view the 3-dimensional models you have to make sure that your WWW browser is configured appropriately. RASMOL is a stand-alone program and has to be installed as a helper application for your WWW browser. CHIME and COSMOPLAYER are available as plug-ins for the standard browsers. Every file delivered by the IMB Jena WWW server is labeled with a MIME type. These MIME types tell your browser how to handle the file. The IMB Jena server stamps RASMOL scripts with the MIME type 'application/x-rasmol'. If you want to view RASMOL scripts you have to make sure that your WWW browser starts RASMOL automatically if a file with the MIME type 'application/x-rasmol' is received. Your browser must be configured to use RASMOL as a helper application for all 'application/x-rasmol' files. If you use NETSCAPE you can change the configuration in the 'Preferences' window. To open this window click on 'Preferences...' in the 'Edit' pull-down menu, and then select the category 'Navigator/Applications'. A detailed recipe for configuring NETSCAPE on a SGI workstation is given in 'Configuring your WWW browser for RASMOL'.

4. MIME types used by the IMB Jena server

The MIME types used by the FLI Jena WWW server are listed in Table 2. If you have problems with receiving files from our server, please check the configuration of your WWW browser. You must install an appropriate plug-in or define a helper application for every type of file which cannot be handled by your browser directly.