VMD-L Mailing List

From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Thu May 28 2015 - 17:29:54 CDT

Hello,

        Here’s another way to see the secondary structure codes:

In the “VMD Timeline” window menu, select:
“Help” -> “Structure codes…”

.
                Cheers,

                Barry

> On May 28, 2015, at 5:14 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
> to your first question:
>
> see fig 9 here:
>
> https://www-s.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline-html/node4.html <https://www-s.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline-html/node4.html>
>
> or page 17 here:
>
> http://www.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline.pdf <http://www.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline.pdf>
>
> for your later question:
>
> when the graph has popped up -- top write corner -
>
> File > Write data file
>
> this will convert the graphical to text format into something like this:
>
> residue|| Chain||some_val||frame number||secondary_structure_Code
>
> Then you can trace a residue's secondary structure state across frame numbers ...
>
> On Fri, May 29, 2015 at 4:21 AM, Jevgenij Raskatov <jraskato_at_ucsc.edu <mailto:jraskato_at_ucsc.edu>> wrote:
> And one more thing, can one actually take this color-coded graph and turn it into numbers, e.g. how many distinct instances along the trajectory does the helical element appear?
>
> On Thu, May 28, 2015 at 9:14 AM, Jevgenij Raskatov <jraskato_at_ucsc.edu <mailto:jraskato_at_ucsc.edu>> wrote:
> Thanks a lot, Ashar; how do I read the color code? I understand that H is helix and C is likely coil, but what about T, E, B, G and I?
>
> Thank you!
>
> On Wed, May 27, 2015 at 7:54 PM, Ashar Malik <asharjm_at_gmail.com <mailto:asharjm_at_gmail.com>> wrote:
> Select Extensions:Analysis:Timeline from "VMD Main" window.
> display a 2D graph of secondary structure vs. time, select Calculate:Calc Sec. Struct. from the "VMD Timeline" window. A color-coded map of secondary structure should appear. The horizontal axis is time (frame number), the vertical axis is residue number/chain.
> Source: http://www.ks.uiuc.edu/Research/vmd/plugins/timeline/ <http://www.ks.uiuc.edu/Research/vmd/plugins/timeline/>
>
>
>
>
> --
> Dr. Jevgenij A. Raskatov
> Assistant Professor in Chemistry and Biochemistry
>
> Tel.: +1-831-459-2978 <tel:%2B1-831-459-2978>
>
> Department of Chemistry and Biochemistry
> Physical Science Building 356
> 1156 High Street
> Santa Cruz, CA
> 95064 USA
>
>
>
> --
> Dr. Jevgenij A. Raskatov
> Assistant Professor in Chemistry and Biochemistry
>
> Tel.: +1-831-459-2978 <tel:%2B1-831-459-2978>
>
> Department of Chemistry and Biochemistry
> Physical Science Building 356
> 1156 High Street
> Santa Cruz, CA
> 95064 USA
>
>
>
> --
> Best,
> /A 

-- 
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