From: Robin Betz (
Date: Wed Jul 18 2018 - 20:14:47 CDT

Hi Kelly,

Secondary structure assignment is done with STRIDE or similar.
You can read how the algorithm functions in the original paper:
Are you recalculating the secondary structure as you go? You can call
"ssrecalc <molid>" in the TCL interpreter to do this and the cartoon
representation will be updated based on the current frame.

More qualitatively, if you remove the restraints from a protein, it then
becomes free to sample more conformations. Some of those conformations may
have fewer helical regions than others. Whether or not those conformations
are valid or relevant is up to you.

Hope this helps,

On Wed, Jul 18, 2018 at 6:08 PM McGuire, Kelly <> wrote:

> This might be a question for the NAMD mailing list as well. I have a
> homotetramer ion channel in a lipid bilayer, and each peptide of this
> channel is completely alpha helical. Sometimes after I minimize, or
> anneal, or equilibrate, or even at my ABF step of the simulation I'll
> notice parts of the alpha helices (new cartoon representation) becoming
> more like the tube representation. During minimization, annealing, and
> equilibration there is a backbone restraint on the protein (none on the
> bilayer, water, or ions), and then at the ABF step, all restraints are
> off. What could be some of the causes for alpha helices in the new cartoon
> representation to shift toward more tube like representations?
> *Kelly L. McGuire*
> *PhD Scholar*
> *Biophysics*
> *Department of Physiology and Developmental Biology*
> *Brigham Young University*
> *LSB 3050*
> *Provo, UT 84602*