VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Jun 22 2007 - 13:10:06 CDT

Hello,

I have a brief question about loading up pdb files in VMD. I noticed
that when I load up a pdb file, one of the atoms is placed at the origin
{0 0 0} and the rest are plotted around that. For instance, for the
simple pdb file:
ATOM 1 H XXX A 1 2.00 2.00 0.00 H
ATOM 2 H XXX A 1 0.00 2.00 0.00 H
END

the fist hydrogen atom is placed at {0 0 2}, the second is placed at {0
0 0}. So the distance between the two atoms is correct, but they're
coordinates are different from what actually appears in the pdb file.

So my question is, how can I load up the pdb file such that the atoms
are placed in the 'absolute' coordinates of file? And how can I do that
from the TCL command line, is there an option to 'mol load pdb
whatever.pdb' ?

Thanks,

Arneh