[Chimera-users] Bonds vs. Pseudobonds

Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner at tugraz.at
Tue Mar 24 09:31:36 PDT 2009

Hello again!

I have a structure containing Germanium bonded to three oxygens and one
methyl group. By default, all of the bonds between Germanium and its
valences are considered as pseudobonds and hence drawn as such.
In the manual, I read that Chimera uses an algorithm that considers
atoms classically bonded if the distance is below the sum of their VDW
radii (plus a margin of 0.4 A). However, no matter what I set the radius
of the Ge atom to (setattr a radius xy Ge), I can't get Chimera to
display a regular bond between Ge and its valences.

Can you give me a hint how to set a rule when a normal bond is drawn, or
how I can draw one manually?

Thank you very much,


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