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From: Barry Isralewitz (barryi_at_ks.uiuc.edu)
Date: Tue Mar 27 2012 - 12:44:38 CDT
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Hi Balaji,
Another approach might be to use the Timeline plugin (Extensions:Analysis:Timeline) which produces 2D plots of this type. Select Calculate:Calc. Sec. Struct. in the Timeline window to view secondary structure. Timeline plots have the bonus of an interactive link to the 3D view -- scrubbing the cursor around an interesting transition in the 2D plot will highlight that residue and frame in the OpenGL 3D molecule view as well as show information about the highlighted object.
Cheers,
Barry
On Mar 27, 2012, at 11:55 AM, Ban Arn wrote:
> Dear VMD users
>
> Recently, I came across the below link and tried to calculate secondary structures for trajectory frames using the tcl script given in the link.
>
> link: http://nefeli.mbg.duth.gr/cgi-bin/wiki.pl/Secondary_structure_analysis_of_protein_trajectories
>
> The script uses vmd for calculation.
>
> The first step works fine and i got the output ss_traj.dat.
>
> In the second step, it shows that using ss_plot it converts ss_traj.dat into post script file.
>
> While using command ss_plot <ss_traj.dat> test.ps, i'm getting error as ss_plot command doesnt found.
>
> I copied & pasted the source code for ss_plot.c in the working directory, still i'm running out of the same problem.
>
> Kindly advice.
>
> Many Thanks
> Balaji
>
>
-- 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
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