From: Axel Kohlmeyer (
Date: Thu Apr 14 2005 - 09:07:57 CDT

On Wed, 13 Apr 2005, Michel Espinoza-Fonseca wrote:

MEF> Hi all,
MEF> I have a very tiny question. Does anybody know how to calculate the
MEF> CA-CA distances between two different residues on a trajectory? I'm
MEF> trying to figure out how to do it, but I don't find the way... All
MEF> comments are welcome!

depending on what you really need,
there may be a _very_ simple solution:

load your molecule and then locate the two CA atoms in question.
now add a line monitoring the distance between those
(type '2' into the OpenGL screen or click on Display->Mouse->Labels->Bonds
and then click on both CA atoms).
now you can already monitor the distance interactively.

if you then go to the Graphics->Labels, select Bonds (instead
of atoms) click on the bond in question in the bluegreen
window so it is highlighted in yellow, click on the graph
tab and the Save... button, you can save the 'trajectory'
of that specific bondlenght to a file.

if you have the xmgrace program installed, you can also
click on the Graph button and xmgrace will be launched
with a plot showing that data, (mostly) ready to be printed.


MEF> Peace,
MEF> Michel

Dr. Axel Kohlmeyer   e-mail:
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum
If you make something idiot-proof, the universe creates a better idiot.