VMD-L Mailing List

From: Florentina Tofoleanu (florentina.tofoleanu_at_gmail.com)
Date: Tue Dec 01 2009 - 12:18:05 CST

John, thank you for forwarding my problem. I was a bit afraid that VMD users
were so bored of this question that they wouldn't answer it anymore. I
haven't got any reply from the author yet, but for me it's an answer worth
waiting for as I'm using VMD so much and I would like it to have the proper
function for saving the secondary structure plots.

Jen, thanks for the script. I haven't used Mathematica before, and it would
take some effort to put it on my Linux machine and learn how to use it, but
I would do it if it comes to it.

On Thu, Nov 26, 2009 at 12:19 PM, Florentina Tofoleanu <
florentina.tofoleanu_at_gmail.com> wrote:

> Dear VMD users,
>
> I have problems with getting a nice colorful plot of the the secondary
> structure of a short peptide during a trajectory. When saving the figure of
> the secondary structure, as many VMD users have probably noticed the axes
> labels are not saved. The same problem as here
> http://ftp.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/10111.html . I sent
> an email to the then enquirer, but no answer. I hoped that VMD 1.8.7 would
> solve the issue, but apparently it hasn't.
>
> Since then, has anyone found a way to save the plots with the labels or to
> plot the data with different labels (like naming the parts of the peptide on
> the y axis etc)? Or has anyone a script to nicely plot secondary structure
> data in the following formats:
>
> 1 A CA 0 C
> 2 A CA 0 C
> 3 A CA 0 E
> 4 A CA 0 E
> 5 A CA 0 E
> 6 A CA 0 E
> 7 A CA 0 E
> 8 A CA 0 E
> 9 A CA 0 E
> 10 A CA 0 E
> 1 A CA 0 C
> 2 A CA 0 C
> 3 A CA 0 E
> 4 A CA 0 E
> .....
> etc (1-10 being the number of residues, repeating for each timeframe)
>
> 1 C C E E E E E E E E E E E E E C C C C C C C E E E E E E E E E C C C E E E
> E E E E E E E...
> 2 C C E E E E E C C C C C C C E E E E E E E E E C C C C E E E E E E E E E E
> E E E E C C C....
> 3 C C E E E E E E E T T C C C C E E E E E E E E E E E E E E C C C C C E E E
> E E E E C C C...
> etc (1,2,3... being the number of frames in the simulation)
>
> Looking more through the VMD-Mailing list I saw some reference to the
> timeline.tcl script. Is anyone more familiar with it to say what to change
> in the script to save the axes labels?
>
> Thank you,
>
> Florentina
>
> --
> Florentina Tofoleanu
> Postgraduate Research Fellow
> Theoretical and Computational Biophysics Group
> University College Dublin
> School of Physics, Rm. 110
> Belfield, Dublin 4, Ireland
> 

-- 
Florentina Tofoleanu
Postgraduate Research Fellow
Theoretical and Computational Biophysics Group
University College Dublin
School of Physics, Rm. 110
Belfield, Dublin 4, Ireland