VMD-L Mailing List

From: Florentina Tofoleanu (florentina.tofoleanu_at_gmail.com)
Date: Thu Nov 26 2009 - 06:19:15 CST

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