VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 31 2011 - 16:18:33 CDT
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Hi,
Actually there is an undocumented way of causing the lines representation
to use a dynamic bond search, by setting the representation from a Tcl
command, adding an extra parameter to set the cutoff distance for the
bond search. I have been meaning to add this to the GUI, but it will
require significant changes to graphical representations window, so
I have been waiting until several new features are exposed in the GUI
at the same time ... but I digress. To enable dynamic bond determination
for the lines rep (and several others), just add the cutoff distance
as an extra representation parameter. For the lines rep you would normally
have a representation command similar to this:
mol modstyle 0 0 Lines 1
To cause it to use dynamic bond determination, add the cutoff, e.g. 1.6A
mol modstyle 0 0 Lines 1 1.6
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Mon, Oct 31, 2011 at 03:32:47PM -0400, Axel Kohlmeyer wrote:
> On Mon, Oct 31, 2011 at 2:21 PM, Bogdan Costescu <bcostescu_at_gmail.com> wrote:
> > Dear vmd-l,
> >
> > I would like to have some kind of DynamicBonds representation, but
> > where the bonds are not represented as cylinders but as Lines. I like
> > how DynamicBonds works, but the representation is slow because there
> > are many cylinders to be drawn. Is there a quick-and-dirty way of
> > combining the two ? I could, of course, just draw the lines myself
>
> no. at least not without changing source code
> and building your own version of VMD.
>
> > from TCL for each frame, but again due to speed reasons I would prefer
> > to use a built-in mechanism.
>
> you can reduce the cylinder resolution to 2 or 3 and diameter to 0.1
> depending on your graphics hardware, turning GLSL on or off might
> speed up things, too.
>
> axel.
>
> > Thanks in advance for any suggestion!
> > Bogdan
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> 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 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
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