VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.wroc.pl)
Date: Sun Apr 21 2013 - 09:44:28 CDT

W dniu 21.04.2013 15:39, Ganesh Shahane pisze:
> I selected "Dihedrals" from the drop down box. But what do you mean by
> "Choose your dihedral label from the list", because I didn't get any
> such list, after selecting "Dihedrals" from the drop down box.
The list of labels of the type selected from the drop down box occupies
the largest field just below the dropdown in this dialog window.
However the field is empty if you haven't defined your labels first -
either using mouse or scripting.
This is described in the vmd user guide, chapter "Labels Form" or so,
feel free to consult it.
Pawel

>
>
> On Sun, Apr 21, 2013 at 6:31 PM, Paweł Kędzierski
> <pawel.kedzierski_at_pwr.wroc.pl <mailto:pawel.kedzierski_at_pwr.wroc.pl>>
> wrote:
>
> W dniu 21.04.2013 09:10, Ganesh Shahane pisze:
>
> Dear all,
> Is there a way to calculate the dihedral angles
> (e.g chi1) of a particular amino acid along the entire
> trajectory using VMD? The angle measures should be presented
> in a graphical format, with the measure of angle on Y-axis and
> time on X-axis.
>
Actually you will have the frame number on the X-axis and you must
calculate time from it based on timestep and the frequency of coordinate
saving.
For example, one may save the data from the plot window "File -> Export
to ASCII matrix" and you will get a text file which can be imported to a
spreadsheet application.

> Yes, and easy.
> First load your trajectory.
> Then make a label on the desired dihedral - use the mouse mode
> "Label -> Dihedrals" from the menu, or key 4.
> Then go to menu Graphics -> Labels, and switch to dihedral labels
> from the dropdown.
> Choose your dihedral label from the list, switch to the "Graph"
> tab, and finally use either "Graph" or "Save" button.
> HTH,
> Pawel
>
>
> --
> Ganesh
> MSc Bioinformatics
> University of Pune.
>
>
>
>
>
> --
> Ganesh
> MSc Bioinformatics
> University of Pune.