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Here are some odds and ends from my past life as a scientist and my present life as a programmer. Come back again and there will be some more stuff as I get to it.

Newmol

Newmol is a primitive but capable biomolecular graphics program. It does two kinds of stereo (cross eyed and straight ahead), generates models for the pov ray tracer, does labels, and allows flexible coloring and display modes (CPK, wire frame, or a combination of both). It only runs on *nixes and has only been tested on linux. The code is butt ugly since I wrote it when I was considerably less experienced. Nevertheless it served me well as a graduate student, so I'm putting it out for others who might be interested. It has no documentation to speak of since I'm too lazy to write any and in truth no longer remember all of the things it does. There is a README that should get you started.

Compact_pdb

Compact_pdb converts big PDB (Protein Data Bank) files into compact binary files that newmol knows how to read. It compresses the entire PDB into about 400Mb of disk space. In the tar ball there is also a script that I use to fetch and compress the entire PDB. Again this only runs on *nixes.

Extract_cpdb

Extract_cpdb converts files from the above compact binary format to regular PDB files. This is for people who already have a molecular graphics program that they like to use. Again this only runs on *nixes. NOTE: I put a fixed version of this up on May 18, 2002. The previous version spat out mirror image pdbs. Doh!

Information

This is a short paper with some useful mathematics for molecular mechanics and molecular dynamics calculations.