Nick's Rose Lab Home Page

Welcome to my home page. While originally intended to be temporary, time constraints and other interests have forced it to be rather permanent. Nothing pretty here--just bare bones information that I needed to put on the web at some point.

While I used to have my email address on this page, countless spammers that crawl through websites searching for email addresses have made that impractical. However, you may reach me by emailing my username (nfitzkee) at this server's address.

Bioinformatics

Click here to visit the introduction to bioinformatics course web site (AS 250.265).

E2SGI Converter

Contrary to popular belief, one does not have to pay StereoGraphics an exorbitant rate to use an old SGI emitter on current Quad-Buffered video card hardware. With a little homework and some soldering, I was able to build their cable for less than $5 using parts that I already had or could cheaply obtain. The major issue is that old SGI Octanes used 12V to power the emitter whereas new systems only supply 5V to the 3-pin mini-DIN. This is remedied in my design using an external power supply, but ostensibly one could hook it up to the PC's internal power supply with only a little more effort.

The cable schematic is available here in PDF format. Email if you have any questions.

Helix Libary

Below is a link to a list of helices I have extracted from the PDB. The file was extracted from PDB files included in the April 2002 PDBSelect list (with a maximum of 25% sequence identity.) Untarring the file can be done like so: 

tar xvfz helixlib.tgz

If you don't have GNU tar (i.e. the z option doesn't autmatically pipe output through gzip), you can use:

gzip -cd helixlib.tgz | tar xvf -

Untarring yields a directory, helixlib, that contains two subdirectories, pdb and ss. Results are stored in additional subdirectories beneath pdb and ss.

pdb
This directory contains in all 7,452 extracted helix PDB's. These results are stored in a heirarchical tree, with directories 0-7 containing approximately 1,000 pdb file extracts. The results are sorted by number, so there isn't necessarily a correspondence between result number and PDB ID. Stored within the PDB file are the coordinate files. Coordinate files all have a SEQRES entry, and REMARK comments indicate the origin of the helix.

ss
This directory is organized like the pdb directory, but rather than containing coordinate files, it contains backbone torsion and secondary structure information. The result numbers correspond to the result numbers in the pdb directory. An ss file contains the following information: each line corresponds to one residue of the helix. The first column is the residue index, and the second column is the amino acid name. The third, fourth, and fifth column store phi, psi, and omega torsions, respectively. The final column stores the secondary structure type (H).

Secondary structure classification was deteremined as described in Srinivasan and Rose, PNAS 96 (1999): 14258.

Download the Helix Library (15 MB)

Wedding Web Page

12/27/2002 - Shortly after Christmas, I asked Jennifer Davis to be my wife. She graciously accepted, and we plan to be married in October of 2003. If you have been given the username and password, you may click here to view the web page containing details for our wedding.