Subject: 1D secondary structure plot

From: Craig Shepherd <[email-masked]>
Date: Tue, 1 Apr 2003 20:45:35 -0700 (MST)

Hi all,

Does anyone know of a tool or viewer which can take a PDB file
and, based on the secondary structure, make a one-dimensional
secondary structure plot?

What I'm envisioning is the type of figures where helices are drawn
as rectangles or cylinders and sheet elements are drawn as arrows.
Some database websites might do this, but ideally I'd like to have
a scalable PostScript plot rather than a rasterized image.

Also, since I'd like to place pictures like this above or below graphs displaying
quantities calculated on a per-residue (or per-atom) basis from an MD simulation
(so as to make clearer which secondary structure elements are involved), I'd like
a standalone tool that could work on an intermediate structure from the simulation,
not just a structure from a database.

Sorry about the length of the message - just wanted to be specific about what I
would ideally like.

Many thanks,

Craig Shepherd