VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Fri Nov 30 2007 - 19:59:40 CST

Axel,

Its me again with more questions... I did not find the Timeline plugin in
the VMD1.8.6 compatible plugins. Could you tell me where to find it? Also,
Timeline seems to work without the plugin, and so in this situation, can I
still edit a timeline.tcl file?

Thanks in advance,
Regards,
Neelanjana

On Nov 30, 2007 5:29 PM, 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 :-)
>
> 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.
> >
>
>
>
> --
>
> 

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