VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Fri Nov 30 2007 - 19:29:49 CST

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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