VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 01 2010 - 17:43:58 CST

Hi,
  You can draw any lines or arrows you like using the VMD "graphics"
or "draw" commands. The people that made the image you referred to
long ago graduated and have since moved on to other institutions,
but the key point is just that they wrote scripts that computed the
line/cylinder endpoints and added them to their molecular rendering to
help illustrate the change in orientation over time.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 01, 2010 at 12:28:22PM +0000, wenchangyu2006_at_gmail.com wrote:
> Thank you, axel. Actually the picture on the webiste is exactly the one I
> want to make. I searched the user guide about "inertia tensor" measurement
> and I think I know how to draw a line in VMD. But I really don't know how
> to transfer the information from inertia to draw the line. I think there
> should be someone in UIUC made the picture when they put the picture on
> the website. Thank you for any suggestion.
>
> Best,
> wenchang
>
> 2010-1-1EIIc,12:57-L-NOTAxel Kohlmeyer <akohlmey_at_gmail.com> *<<D-'-L--o
> > please always keep the mailing list in cc: so that
> >
> >
> > people on the list get to see, if a request has been
> >
> >
> > answered sufficiently or not.
> >
> >
> >
> >
> >
> > 2009/12/31 wenchangyu2006_at_gmail.com>:
> >
> >
> > > Thank you, axel. Actually I would like to how to draw the lines in
> that
> >
> >
> > > picture on the website. I think this is the direction of the protein
> moving
> >
> >
> > > and this can be done by script programming, which I want to know.
> Thanks.
> >
> >
> >
> >
> >
> > if you want to know about those lines, why don't you ask about it in
> >
> >
> > the first place. please keep in mind that an answer to a question can
> >
> >
> > only be as good and accurate as the question itself.
> >
> >
> >
> >
> >
> > those lines look like some position vectors of the principal axis to me
> >
> >
> > that were derived from the inertia tensor at different time steps, where
> >
> >
> > the color encodes the time.
> >
> >
> >
> >
> >
> > of course that can be scripted. again, please see the user's guide
> (graphics
> >
> >
> > commands). since this kind of imagery cannot be easily generalized,
> you'll
> >
> >
> > have to sort out the details by yourself.
> >
> >
> >
> >
> >
> > cheers,
> >
> >
> > axel.
> >
> >
> >
> >
> >
> > > 2009-12-31IAIc,10:08-L-NOTAxel Kohlmeyer akohlmey_at_gmail.com>
> *<<D-'-L--o
> >
> >
> > >> On Thu, Dec 31, 2009 at 6:47 AM, O:U:IA:^2y wenchangyu2006_at_gmail.com>
> wrote:
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> > Hi,
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> > Does anybody know how to make the example on VMD website, titled
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> > "Superposition of Multiple Trajectory Timesteps " in the following
> link?
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> > http://www.ks.uiuc.edu/Research/vmd/allversions/repimages/#examples
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> >
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> > I appreciate if anybody can give some suggestions, thank you and
> Happy
> >
> >
> > >> > New
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> > Year
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> how about reading the VMD user's guide?
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> particularly the part about the contents of the
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> trajectory tab in the graphical representations dialog.
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> cheers,
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> axel.
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> > wenchang
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> --
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> Institute for Computational Molecular Science
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> College of Science and Technology
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >> Temple University, Philadelphia PA, USA.
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> > >>
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> >
> >
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> >
> >
> > Institute for Computational Molecular Science
> >
> >
> > College of Science and Technology
> >
> >
> > Temple University, Philadelphia PA, USA.
> >
> >
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078