From: Axel Kohlmeyer (
Date: Mon Jun 23 2008 - 10:13:41 CDT

On Mon, 23 Jun 2008, wrote:

YW> Dear all,
YW> I want to visualize a PDB file containing chlorine "CL" and iron "Fe" atoms.
YW> But VMD seems made a mistake to recognize "CL" to be "C" (carbon), and "Fe" to be fluorin "F".
YW> Could anyone tell me how to visualize these atoms properly?

please explain what you mean by "properly"?

VMD does not care at all about the chemistry and
the consequence of "guessing" is only the color
and the element entries. both can be changed by
using short tcl scripts. if you have a standard
compliant PDB file, VMD should actually get the
element information right as it is part of the
PDB standard.

YW> Any response will be greatly appreciated.
YW> Yong Wang
YW> ___________________________________
YW> DICP WebMail,

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.