VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sat Dec 01 2007 - 08:05:39 CST

On Dec 1, 2007 2:29 AM, Neelanjana Sengupta <senguptan_at_gmail.com> wrote:
> Dear Axel,
>
> Thanks for the pointers... this gives me a lot of info! As of now, I have
> been able to use the Timeline for getting the Secondary Structure (that's
> what I need for now). Is it true that the color scheme of timeline is the
> same as that of sequence viewer (ie., green--Turn; white--Coil;
> magenta--Alpha hlx; light pink--310 hlx)? Also, I am getting some blue in
> my timeline, and I don't know what that stands for... some more info would
> be highly appreciated :-)

Blue is 3-10 helix.

>
> Regards,
> Neelanjana
>
> On Nov 30, 2007 1:31 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> > 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.
> >
>
>
>
> --
>
>