VMD-L Mailing List

From: Santanu Santra (santop420_at_gmail.com)
Date: Tue Sep 28 2021 - 00:37:42 CDT

hi Barry,
Thanks a ton for your kind help.
regards
Santanu

On Tue, Sep 28, 2021 at 4:44 AM Isralewitz, Barry <isralewi_at_illinois.edu>
wrote:

> Hi Santanu,
>
> For plotting time-dependent secondary structure information of
> trajectories loaded into VMD, consider the Timeline plugin. Access with:
> VMD Main window, Extensions:Analysis:Timeline
>
> Tutorial:
> https://www.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline.pdf
> More at: https://www.ks.uiuc.edu/Training/Tutorials
>
>
> Cheers,
> Barry
>
>
>
> On Sep 25, 2021, at 10:22 AM, Santanu Santra <santop420_at_gmail.com> wrote:
>
> Dear all,
>
> I am able to generate *.stride output files for multiple pdb files. For a
> single file VMD is able to generate color map for showing each residue
> belong to either helix, 3-10 helix, sheet , coil etc. But I need to plot
> for multiple pdb files like time frame 1, 2,3, 4 etc upto 100 ns.
> N.B. I am using sequence generator option in VMD.
>
> 5|
> 4|
> Residue 3|
> 2|
> 1|
> ---1---2---3---4---5---6----------------------------
> time
> Please help me to generate a plot of time dependent secondary structure
> information from multiple pdb files or dcd file by stride program.
>
> Any kind of help is highly appreciated.
> thanks
>
>
> --
> Santanu Santra
>
>
> --
> Barry Isralewitz
> Theoretical and Computational Biophysics Group
> 3043 Beckman, University of Illinois at Urbana-Champaign
> Office Phone: (217) 244-1612
> Email: isralewi_at_illinois.edu <isralewi_at_illinois.edu>
> http://www.ks.uiuc.edu/~barryi
>
>
>
>
>
> 

-- 
Santanu Santra
Research Scholar
Molecular Simulation Laboratory
Department of Chemistry
NIT ROURKELA
ROURKELA, 769008