VMD-L Mailing List

From: Karsten Suhre (Karsten.Suhre_at_igs.cnrs-mrs.fr)
Date: Thu May 06 2004 - 01:44:52 CDT

> This is sort of a beginner's question ... I tried loading in the
> attached pdb file into VMD, but I couldn't see any bonds. This is the
> file used for Rasmol, and all three different atoms and bonds could be
> seen in Rasmol. Am I missing something?
> Any advice would be greatly appreciate!

The distances between your atoms are too large. There is a parameter "distance
cutoff" to the representation type "dynamic bonds". If you select this
representation and a cut-off larger than 2.6 the bonds will appear for your
molecule. You can then add a second rep (using the "Create Rep" button in the
"representations" menu) and select representation type VDW (reduce the Sphere
Scale a bit). This will give you a nice view (I attach the vmd script to this
mail, run it using the command "vmd -e InGaAs.vmd").

 Kind regards, Karsten.