From: Ashar Malik (
Date: Fri Jul 10 2015 - 11:21:09 CDT

A primary structure is not a structure per say -- I am guessing what you
want is the same helix in an unfolded state -- ??

The easiest way to do this would be to use advanced visualizer that allows
you to draw molecules.

One choice among many would be

you can just create a rigid polypeptide chain of the sequence that
constitutes your helix.

On Sat, Jul 11, 2015 at 3:45 AM, Jinasena Hewage <> wrote:
> I have a secondary structure (apha-helix) obtained from a protein data
> base. I want to convert it to a primary (liner structure).
> Is there way of doing it in VMD or by using a  tcl script.
> Hewage
> --
> Dr. Jinasena Hewage
> Senior Lecturer  in Physical Chemistry
> (Current Position: Visiting Academic, Research School of Chemistry,
> Australian National University)
> Department of Chemistry
> University of Ruhuna
> Matara, Sri Lanka
> (+94) 071 4500 389