VMD-L Mailing List

From: Bernhard Knapp (bernhard.knapp_at_meduniwien.ac.at)
Date: Tue Dec 16 2008 - 03:30:03 CST

Hi everyone

Does anybody of you know how the alpha helix structure in new cartoon
representation is defined in vmd? Which angles and distances are
necessary between which atoms? I am asking because during a molecular
dynamics simulation the alpha helical structure of a MHC gets destroyed
and I am wondering at which threshold it is not represented as alpha
helix anymore? Unfortunately I could not find the answer neither in vmd
reference nor in the user documentation.

cheers

Bernhard