VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Dec 01 2007 - 18:33:58 CST

On Fri, 30 Nov 2007, Neelanjana Sengupta wrote:

NS> Axel,
NS>
NS> Its me again with more questions... I did not find the Timeline plugin in
NS> the VMD1.8.6 compatible plugins. Could you tell me where to find it? Also,

timeline is part of the VMD distribution. no additional installation is
required. the timeline.tcl file is somewhere in the vmd library
directory in plugins/noarch/tcl/timeline1.0/

NS> Timeline seems to work without the plugin, and so in this situation, can I
NS> still edit a timeline.tcl file?

if you locate the file, you can edit it. it _is_ a text file.

cheers,
   axel.

NS> Thanks in advance,
NS> Regards,
NS> Neelanjana
NS>
NS> On Nov 30, 2007 5:29 PM, Neelanjana Sengupta <senguptan_at_gmail.com> wrote:
NS>
NS> > Dear Axel,
NS> >
NS> > Thanks for the pointers... this gives me a lot of info! As of now, I have
NS> > been able to use the Timeline for getting the Secondary Structure (that's
NS> > what I need for now). Is it true that the color scheme of timeline is the
NS> > same as that of sequence viewer (ie., green--Turn; white--Coil;
NS> > magenta--Alpha hlx; light pink--310 hlx)? Also, I am getting some blue in
NS> > my timeline, and I don't know what that stands for... some more info would
NS> > be highly appreciated :-)
NS> >
NS> > Regards,
NS> > Neelanjana
NS> >
NS> >
NS> > On Nov 30, 2007 1:31 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
NS> > wrote:
NS> >
NS> > > On Fri, 30 Nov 2007, Neelanjana Sengupta wrote:
NS> > >
NS> > > NS> Dear VMD experts,
NS> > >
NS> > > dear neelanjana,
NS> > >
NS> > > NS> I have a very long simulation of an 8-residue peptide, and would
NS> > > like to see
NS> > > NS> the (phi,psi) angle of each residue as a function of time. I am
NS> > > trying to
NS> > > NS> use VMD's 'Timeline', and I face these issues:
NS> > > NS>
NS> > > NS> a) On first loading my .psf, then opening Timeline, I choose
NS> > > File>print to
NS> > > NS> file; Calculate>phi; Appearance>(color purple and the angle range).
NS> > > Then I
NS> > > NS> load my .dcd file. However, nothing happens in the time line viewer,
NS> > > and the
NS> > > NS> file written out is also a blank file. Can I get some pointers here,
NS> > > as I
NS> > > NS> did not find instructions in the VMD User's guide?
NS> > >
NS> > > not all plugins are written in a sophisticated enough way to notice
NS> > > changes in the number of frames and/or molecules while they are open.
NS> > > the timeline plugin has not been significantly updated for a long time
NS> > > (judging from the development log, a new version is coming, though).
NS> > > have you tried loading .psf and .dcd _first_ and then open the timeline
NS> > > viewer?
NS> > >
NS> > > NS> b) Are purple and yellow the only colors available?
NS> > >
NS> > > the colors are supposed to match the default colors of the
NS> > > "Structure" Colorization scheme. if you want to change them,
NS> > > you can edit the timeline.tcl file (search for "purple" and
NS> > > it will take you to the right block in the input. (the ideal
NS> > > situation would of course be that the timeline.tcl script
NS> > > would take those values from the corresponding color table
NS> > > entry and thus changing the structure colors would also
NS> > > change them in the timeline plugin. hint. hint!!).
NS> > >
NS> > > NS> c) I find it a little unusual that it can calculate (delta_Psi), but
NS> > > not
NS> > > NS> just the dihedral psi... are they the same? If not, is there a way I
NS> > > can get
NS> > > NS> the timeline for the Psi angle too?
NS> > >
NS> > > i guess the programmer of timeline.tcl should comment on this
NS> > > (hope he is subscribed here ;-) ).
NS> > >
NS> > > cheers,
NS> > > axel.
NS> > >
NS> > >
NS> > > NS>
NS> > > NS> Thanks in advance,
NS> > > NS> Regards,
NS> > > NS> Neelanjana Sengupta
NS> > > NS> --
NS> > > NS>
NS> > >
NS> > > --
NS> > > =======================================================================
NS> > > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
NS> > > Center for Molecular Modeling -- University of Pennsylvania
NS> > > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
NS> > > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
NS> > > =======================================================================
NS> > > If you make something idiot-proof, the universe creates a better idiot.
NS> > >
NS> >
NS> >
NS> >
NS> > --
NS> >
NS> >
NS>
NS>
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.