What is the 'VRML File Creator for Chemical Structures'?

The VRML File Creator for Chemical Structures is an online service for the generation of VRML scenes from your 2D or 3D data files. It supports over 40 structure file formats and contains also a Molecule editor for structure input. It automatic generates 3D coordinates if not contained in the input structure. It has many display options to control the visual appearance.

The service was developed within the framework of the ChemVis research project. ChemVis

What is VRML?

VRML is the Virtual Reality Modelling Language, a standard for the distribution of 3D scenes. If a VRML link is selected, your browser retrieves the scene file and passes it to an external viewer or a plug-in. VRML files can themselves contain links to other scenes, ultimately building a sub-web. Since a VRML browser can follow all VRML links autonomously, a purely virtual 3D information space without flat HTML pages is theoretically possible.

The advantage of distributing 3-dimensional data by means of VRML scenes is that you are no longer dependent on specific hardware or software. VRML is platform-independent and browsers exist for all major platforms. In contrast to Chemical MIME (i.e. sending structure files which are visualized by molecule viewers such as RasMol) the author of a scene has full control of the appearance. All geometric primitives, color, lights, cameras are predefined, and the display style is fixed. Once a scene has been downloaded, it can be examined from all sides and even walked through. The actual VRML version (VRML 2.0) now supports advanced possibilities to achieve realtime user interaction and context driven 3D animation inside the VR scene (e.g. manipulations, calculations).

Reconstructing semi-automatically chemical information from VRML scenes, which could be reused and whose data could be re-analysed in detail, is possible as well (see Structure code in the Help page).

How can I view VRML scenes?

You need a VRML browser or plug-in (such as Cosmo Player) installed on your computer. If you use a plug-in, you probably will not need any additional configuration. If you rely on an external viewer, the .mailcap file in your home directoy or in the system directory probably needs to be adapted. This file controls which viewer the HTML browser should start when certain MIME-compliant types of files are received, which the HTML browser cannot handle itself. The file must contain a line like

		model/vrml;  i3d -remote 'openURL(%s,%u)'
The example line is for the i3D client for Silicon Graphics machines. The details of the installation process are dependent on the type of operating system and the viewer you are using. If you cannot manage the set-up yourself, contact your system administrator.

Get the latest version of Cosmoplayer here. Cosmo Player

Try this link in order to check your setup. A methane molecule in Ball&Stick representation should appear.

methane screenshot

Where can I get more information?

How can I generate VRML from molecular data ?

Well, currently there are not too many possibilities I know about. If you use other programs or services, please tell me about it.

  • The xtal-3d program can be used to generate VRML from a number of standard crystallographic formats. An interactive WWW-based version is also online.
  • The pdb2vrml program converts PDB files to VRML. An interactive WWW-based version is also online.
  • The CACTVS system molecule editor supports VRML output in V2.14 and beyond.
    It is now released to the public!
    The VRML generation routines used in this program are the same as on this page, which is a test application for them. Note that in order to generate VRML scenes with this editor, you either must provide input data which already contains 3D atomic coordinates or obtain a CORINA 3D coordinate generation module license, since the editor allows only the drawing of 2D structure plots and must compute 3D coordinates for all output formats which require them - among them VRML, but also PDB and XYZ.
  • And there is our new service on this page.
    Just select the desired plot style, provide a structure as SMILES string (the prepared demo string in the entry field is cubane), as a structure file or with the help of the Java Molecule Editor, press the 'Submit' button, and the VRML scene is returned immediately.

Usage conditions

You can use the images generated by this service free of charge for every purpose you can imagine. If you put them on a Web site, the HTML document embedding the VRML file must contain a link to this page. A small footnote is sufficient. After some bad experiences with other free data we provided to the Internet community, you are explicitly forbidden to include these scenes in any CD or other medium you charge for without prior contact and an agreement in writing.

We will treat the structures confidentially, but they travel unencrypted on the Internet, and we log them to evaluate program performance.

F. Oellien

Last Update: 2018-01-12