VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Nov 30 2007 - 15:31:56 CST

On Fri, 30 Nov 2007, Neelanjana Sengupta wrote:

NS> Dear VMD experts,

dear neelanjana,

NS> I have a very long simulation of an 8-residue peptide, and would like to see
NS> the (phi,psi) angle of each residue as a function of time. I am trying to
NS> use VMD's 'Timeline', and I face these issues:
NS>
NS> a) On first loading my .psf, then opening Timeline, I choose File>print to
NS> file; Calculate>phi; Appearance>(color purple and the angle range). Then I
NS> load my .dcd file. However, nothing happens in the time line viewer, and the
NS> file written out is also a blank file. Can I get some pointers here, as I
NS> did not find instructions in the VMD User's guide?

not all plugins are written in a sophisticated enough way to notice
changes in the number of frames and/or molecules while they are open.
the timeline plugin has not been significantly updated for a long time
(judging from the development log, a new version is coming, though).
have you tried loading .psf and .dcd _first_ and then open the timeline
viewer?

NS> b) Are purple and yellow the only colors available?

the colors are supposed to match the default colors of the
"Structure" Colorization scheme. if you want to change them,
you can edit the timeline.tcl file (search for "purple" and
it will take you to the right block in the input. (the ideal
situation would of course be that the timeline.tcl script
would take those values from the corresponding color table
entry and thus changing the structure colors would also
change them in the timeline plugin. hint. hint!!).

NS> c) I find it a little unusual that it can calculate (delta_Psi), but not
NS> just the dihedral psi... are they the same? If not, is there a way I can get
NS> the timeline for the Psi angle too?

i guess the programmer of timeline.tcl should comment on this
(hope he is subscribed here ;-) ).

cheers,
   axel.

NS>
NS> Thanks in advance,
NS> Regards,
NS> Neelanjana Sengupta
NS> --
NS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.