VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Dec 01 2009 - 10:53:00 CST

Hi,
  I think that saving the plots with different labels/captions etc
would currently require modifying the Timeline plugin's script code.
I will forward your note to the author of the Timeline plugin and see
if he has any suggestions about this, but in the case of an
absence of suggestions you may simply want to try modifying the script
to get it to do what you want.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 26, 2009 at 12:19:15PM +0000, Florentina Tofoleanu 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078