404 Object Not Found

404 Object Not Found

Visualization of Molecular Geometry using VRML

The program PDB2VRML converts molecular structure information stored in a Brookhaven Protein Database file (.pdb) into a VRML world file (.wrl).

The current version of PDB2VRML.EXE (version 1.4) is written in C and runs from the command line under Windows (Pentium processor required).

The PDB2VRML program was written by David N. Blauch (© Copyright 1998-2001 David N. Blauch). The program may be freely distributed but may not be altered or revised. The program may not be resold. Users assume any and all responsibility for any damages or liabilities resulting from this program.

Download PDB2VRML.ZIP (116 Kb) (version 1.4)

Version Information

Version 1.4

• Removed the previous options to rotate independently around the x, y, or z axis. The current feature allows the user to define an arbitrary axis of rotation and rotation angle.
• Added information for additional atoms.
• Program now produces smaller VRML files that should load and execute faster.

Version 1.3

• Adjusted the colors of several atoms to coincide with CPK colors.

Version 1.2

• Repaired a bug in calculating the rotation information that resulted in a floating point error.
• Expanded the number of atoms (now 24) for which the CPK color, covalent radius, and van der Waals radius is defined.

Version 1.0

• Program recognizes only ATOM and CONECT tags.
• If no CONECT tags are present, bonds are automatically created between atoms that are sufficiently close to each other. This option can be disabled. It can also be invoked even when CONECT tags are present.
• Display options include Ball-and-Stick, Space-Filling, and Wire-Frame.
• Molecules are automatically centered about the origin and the viewing frame is set to contain the entire molecule. This option can be disabled.

Demos

A VRML viewer such as SGI Cosmo Player is required. The VRML viewer provides controls that affect your movement, not that of the object you are viewing (with the exception of the rotate or examine control). Dragging the mouse left (with the left button pressed) moves you left, making it appear that the object is moving right. The examine or rotate control (which may require moving a "gear shift" in some viewers) permits you to rotate the object. The point around which rotation occurs varies from viewer to viewer.

The PDB2VRML program has been used to generate VRML files depicting the molecular structure of a polyproline molecule. The polyproline molecule is displayed in three different formats:

• Ball and Stick
• Space Filling
• Wire Frame

404 Object Not Found

404 Object Not Found