COORDCOMP

Cartesian All Atom Coordinate Comparison

Plots the absolute distance between like atoms in two PDB files as shown below. The filled circles represent the distances between respective alpha carbons in the two files. The open circles represent distances between respective side chain and other backbone atoms in the two files.

• The PDB files must have identical order of atoms.
• It makes sense only for structures superpositioned by CA atoms. (Use for example "lsqman").
• For site mutations edit the PDB files so that the mutated site only has CB for the side chain (or none if GLY).

Save a copy of the coordcomp script to your computer and make it executable.

To use coordcomp copy the script to your current directory with the two superpositioned structures and type:

coordcomp PDBfilename1 PDBfilename2

A plot similar to the one above should appear on your screen if you are local. The results are deposited in three files in your current working directory for alternate analysis:

1. dist.list - Distances between the same respective atom in each PDB file.
2. dist.plt - A data file useful for plotting the data using your favorite program.
3. dist.param - Parameter file for displaying dist.plt in XMGR

Please send comments/problems to Pat Fleming.