From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Mon May 07 2012 - 12:32:42 CDT

Hi,

        Timeline (like the rest of VMD) uses STRIDE to calculate secondary structure. Reference for STRIDE: Frishman,D. & Argos,P. (1995) Knowledge-based secondary structure assignment. Proteins: structure, function and genetics, 23, 566-579.

In the "VMD Timeline" window menu bar, select:
"Help":"Structure Codes…"
to see the list of structure codes.

        You should see this displayed:

=================
Secondary Structure Codes

T Turn

E Extended conformation

B Isolated bridge

H Alpha helix

G 3-10 helix

I Pi-helix

C Coil (none of the above)
=================

        Cheers,

        Barry

On May 7, 2012, at 11:10 AM, santhu kumar wrote:

> Hey Albert,
>
> DSSP has classified secondary structure elements into different categories. I would think they represent it.
>
> http://en.wikipedia.org/wiki/Protein_secondary_structure : Look into the DSSP code.
>
> Cheers,
> Santhosh
>
> On Mon, May 7, 2012 at 10:07 AM, Albert <mailmd2011_at_gmail.com> wrote:
> hello:
>
> I've plot the 2nd structure by Time-line in VMD 1.91. and I found the plot is in different colors. What does those corresponding letter caption for different colors such as:
>
> T E B H G I C ?
>
> probably B for beta-strand and H for Helix? what about the left?
>
> thank you very much
> Albert
>
>
>

-- 
Barry Isralewitz
Theoretical and Computational Biophysics Group
3043 Beckman, University of Illinois at Urbana-Champaign
Office Phone: (217) 244-1612
email: barryi_at_ks.uiuc.edu   http://www.ks.uiuc.edu/~barryi