Generating Primary and Secondary Structure Models using VMD

Goals

Given a PDB file, we want to generate geometry files that can be read into perfly. For our demo, we had a sequence of PDB formatted .coor files generated by NAMD. By turning these into a sequence of .iv files, we can create an animation in perfly_ccv.

Tools

The tool I'm using is VMD from the Theoretical Biophysics Group at the University of Illinois at Urbana-Champaign. I'll be using the built-in tcl interpreter to automate generating geometry for each frame in the dynamics animation.

As it turns out, the other tools necessary for this to work have yet to be developed. We still need:

A tool that converts STL to raw format. This isn't too complicated since part of the STL format is a list of vertices for each triangle. Vinay started work on a quick version of this on 05/09/02. Once we have a .raw file, there is a tool to convert to .iv format (raw2iv).
We also need a tool to convert VRML-1 to .iv (Inventor) format. I don't think anyone's started work on this as of yet.

Progress

The tcl script for generating models in VMD is done. To use it, you have to modify a few values as described in the comments in the script. The arguments to the mol rep and mol color statements in the script can be set to any of the strings in the Coloring Method and Drawing Method drop down lists, respectively, in the Graphics dialog in VMD. The first arguments to the render statements specify the output file format and can be any of the strings from the Output Formats list on the Render dialog.

Todo List

Finish the STL to raw format converter. This will allow us to finish the PDB->STL->RAW->IV conversion path to getting the data into perfly.
Write the VRML-1 to Inventor format converter. This is only needed because the STL rendering method in VMD only outputs triangles. This means that the secondary structure (or Cartoon) representation of the molecule can be rendered this way, but the CPK and VDW representations use sphere and cylinder primitives that aren't translated by the STL rendering method. The VRML-1 rendering method uses the sphere and cylinder primitives, so with a conversion from VRML-1 to Inventor we never have to convert these primitives into triangles.

Originally written on 05/10/2002.
Dave Harding