From: Axel Kohlmeyer (
Date: Tue Jan 27 2009 - 08:35:34 CST

On Tue, 27 Jan 2009, Javier Goicochea wrote:

JG> Hello All,

hello javier.
JG> I have noticed that most PDB files provide different name to atoms in the
JG> same structure or molecule. These names are set to identify (up to some
JG> extend) their relation with other atoms and connectivity. My questions are:
JG> Is VMD tie in anyway to a particular naming convention?

yes and no. in principle VMD itself knows nothing about chemistry
and doesn't really care internally. but some analysis and "service"
routines as well as scripts and plugins make some assumptions that
depend on the context they are written for.
JG> Which naming convention is used typically in the PDB files?

please have a look at the pdb standard. or stick
"pdb atom naming conventions" into google and in
combination with an introductory biochemistry text
book, you should be able to figure it out.

JG> Where do I find this naming convention (book, publication), if any?

see above.

JG> Let mention that I am neither a Chemist nor a Biologist, just a Mechanical
JG> Engineer with little experience in VMD.

please note that this is no excuse for not having tried to look
stuff up in a web search engine (e.g. google) or wikipedia. ;)

especially, since most of the questions are about the PDB file format,
which is not defined by VMD.


JG> Thank you in advance, Javier

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.