From: Axel Kohlmeyer (
Date: Tue Apr 11 2006 - 14:11:13 CDT

On Tue, 11 Apr 2006, Kenley Barrett wrote:

KB> Dear VMD users,
KB> I have two (similar) questions. First, when you use the "label --> atoms"
KB> mouse command to click on two atoms and measure the distance between them,
KB> what exactly is the distance measured? Is it the distance between the
KB> centers of the atoms, or is it the distance between the edges of the van der
KB> Waals radii? Second, when I use the command "within 5 of resid 1" under
KB> "Graphical Representations", which atoms am I displaying? Am I displaying
KB> atoms whose centers are within 5 angstroms of the center of any atom in
KB> residue 1, or am I displaying atoms whose van der Waals radii come within 5
KB> angstroms of the van der Waals radius of any atom in residue 1?


in both cases, this is always referring to the atom centers. this is
all the distance code in VMD knows about. the vdW radius is added later.

if you have doubts, just create some simple test files
and see for yourself.

best regards,

KB> Please let me know any information that you may have. Thank you very much in
KB> advance for your help.
KB> Sincerely,
KB> Kenley Barrett

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.