VMD-L Mailing List

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Tue Apr 11 2006 - 11:19:41 CDT

Dear VMD users,

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

Please let me know any information that you may have. Thank you very much in
advance for your help.

Sincerely,
Kenley Barrett