VMD-L Mailing List

From: Rogan Carr (rogan_at_ks.uiuc.edu)
Date: Wed Apr 22 2009 - 11:29:32 CDT

Hi Bin,

If you just need to visualize the restraints, why don't you use 'draw'
commands? Check out the Images and Movies tutorial for drawing arrows
and such on the fly.

http://www.ks.uiuc.edu/Training/Tutorials/vmd-ref/imgmv/tutorial-html/index.html

Rogan

On Apr 21, 2009, at 11:48 PM, zhngbn_at_gmail.com wrote:

> Hi, John:
>
> Thanks a lot for your comment.
>
> I'm actually trying to visualize some of the harmonic restraints
> applied for a particular atom.
>
> Thank,
> Bin
>
>
> On Apr 21, 2009 9:44pm, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> > Hi,
> >
> > For performance and memory consumption reasons, VMD uses a
> >
> > fixed-sized bond list for each atom. The standard VMD builds
> >
> > limit the maximum number of bonds for a single atom to 12.
> >
> > If you have a genuine need to define more than 12 bonds for a
> >
> > single atom, VMD can be built to allow a larger maximum
> >
> > value, by editing the definition of the MAXATOMBONDS macro
> >
> > at the top of Atom.h and recompiling the source code.
> >
> >
> >
> > What kind of structure are you working with such that you need
> >
> > so many bonds?
> >
> >
> >
> > Cheers,
> >
> > John Stone
> >
> > vmd_at_ks.uiuc.edu
> >
> >
> >
> > On Tue, Apr 21, 2009 at 09:01:35PM -0700, BIN ZHANG wrote:
> >
> > > Dear All:
> >
> > >
> >
> > > While I was using the "setbonds" command in VMD, I got the
> following
> >
> > > error:
> >
> > >
> >
> > > atomsel: setbonds: too many bonds in bondlist: 402 404 406 468
> 284 418
> >
> > > 414 416 227 420 470 411 409
> >
> > > Maximum of 12 bonds
> >
> > >
> >
> > > I wonder why would this be necessary? Is there anyway to turn it
> off?
> >
> > >
> >
> > > Thanks,
> >
> > > Bin
> >
> > >
> >
> >
> >
> > --
> >
> > 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
> >