MolVRML: build VRML models of 3D molecular structures

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Introduction

The protein data bank [1] is a public database for depositing 3D biological macromolecular structure data. It is a core database for research and education in biology, chemistry and medicine.

The 3D structure files can be downloaded in PDB file format. It is a text file with extension .pdb, and contains 3D coordinates of atoms. The PDB format is widely supported by various 3D visualization and/or modelling applications.

VRML (Virtue Reality Modelling Language) is originally developed for display 3D graphics on the Internet. VRML models can be displayed in both Internet web browsers and Microsoft office programs with VRML plugin. The Web3D Repository [2] maintains a list of VRML plugin. A website at National Institute of Standard and Technology [3] will be able to detect whether a browser has VRML plugin, and also contains links to the popular VRML plugin such as Cosmo player [4] and Cortona VRML Client [5]. The Cortona VRML Client also works in the commonly used programs such as Microsoft Word, PowerPoint, Excel and Access on the Window platform. Incorporating alive 3D scenes in Word documents or PowerPoint presentations may enhance the effectiveness of describing 3D molecule structures.

OpenVRML is developing a program -- LookAt[6], which is a standalone application for display VRML scenes, and it can run on the Linux, Unix, Window and Mac platform.

In order to display 3D molecule structure with VRML viewer, the PDB files need to be transformed into VRML 3D scenes.

Brief Review of Available Programs

There are a few tools available to convert PDB file into VRML 3D models. Each tool is briefly described as follows.

A small Perl script named pdb2vrml.pl [7] is open source. It appears this script only converts PDB into VRML 1.0 and the conversion is limited in the space fill model.

A free Window executable called pdb2vrml.exe [8] is distributed at the version 1.4. The program is written in ASCII C by David N. Blauch. It converts PDB into VRML 2.0 in space fill, ball stick and wire frame model. However so far it only works from Window prompt or command.

A free Unix/Linux binary, pdb2vrml [9] is available from Institute für Physikalische Chemie. The authors also provide a web interface for converting PDB to VRML. [10]

A small open source C++ library, pdb2vrml, was created by Vieri Di Paola. [11] It is incomplete and not well maintained since 1997.

A program called MolScript, [12] that is developed in ASCII C and the older version 1.4 or earlier were written in Fortran 77. The source code and Unix binary are distributed under licenses. The MolAuto component in the MolScript can generate VRML presentation of 3D structure. The MolScript is powering the VRML web interface at the protein data bank [1].

There are a few online conversion services via a web interface. The ChemVis [13] project provides an online VRML file creator, allows user to input a PDB file. The protein data bank has a default 3D viewer in VRML and also provide a more detailed VRML file rendering.

The softwares such as Spartan [14], MOLDEN [15] and Molda [16] provide function of saving 3D scenes into VRML file.

In summary, a cross-platform application with easy-use graphic user interface for converting PDB to VRML is currently unavailable. Therefore the author aims to develop a platform independent standalone program with a graphic interface in Java.

MolVRML

Figure 1. A Screenshots Shows MolVRML 2.0.

Features of MolVRML

The first appearance is a small and informative splash screen at the time of loading MolVRML. Then the MolVRML window is fully displayed and waiting for user interaction. The built-in help data will guide user at various stages as needed. When one of four "life" buttons (butterfly, fish, eagle and swallow button for space fill, wire frame, ball stick and bond mesh model conversion respectively) is clicked the model dialog window will appear. All the parameters in association with file conversion are taken from this window. The strict validation and error massage display are taken place here, and any possible combination of conditions is taken into account. Once the validation is success the parameters are passed into relevant routines, at the meantime a working sign at the progress bar appears. After the conversion complete, the file path of PDB and VRML files as well as other information will be displayed on the text area on the MolVRML window.

In the version 2.0, the temperature factor, hydrogen bonds and salt bridges are not taken into consideration. Only the first structure model will be converted if the PDB file contains more than one structure model. Normally multiple structure models are deposited in the NMR determined structure entries. If user is interested in a particular structure model rather than the first one the desired model could be copied out and save in a text file with extension .pdb or .ent, then convert this file with MolVRML.

References

1. Protein Data Bank: the single worldwide database for depositing 3D structures of biological macromolecules
2. A list of VRML plugins at the Web3D Repository
3. VRML Plugin and Browser Detector
4. Cosmo Player:the first developed VRML browser plugin
5. Cortona VRML Client:run on Windows, Mac and CE
6. LookAt:a standalone VRML viewer for Linux/Unix, Window and Mac platforms
7. Pdb2vrml.pl:a small open source Perl script
8. Pdb2vrml.exe:a free executible for Windows
9. PDB to VRML Converter:a free Linux/Unix binary
10. PDB Visualization:a web interface for converting PDB to VRML
11. PDB to VRML Converter Library:an incomplete open source C++ library
12. MolScript:a licensed C code and free Unix binary
13. ChemVis Projects and Services:a web interface for PDB to VRML conversion
14. Spartan:a 3D molecule view program
15. MOLDEN:a 3D molecule view program
16. Molda:a 3D molecule view and modelling program

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