From: snoze pa (snoze.pa_at_gmail.com)
Date: Thu Jan 10 2008 - 10:45:28 CST

Yeah, it is bond but defined as LINK in PDB file format. Unfortunately I do
not have the connectivity information so I want to draw a usr defined bond.
Similar question is lying in vmd mailing list but in different context.
Here is the link

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4946.html
I am sorry if you guys find the "LINK" complicated. Thanks for sharing your
valuable time.

On Jan 9, 2008 10:51 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> You haven't explained what you mean by "linked"...
> Do you mean that the atoms are shown to be bonded? Please be more
> clear about what you're wanting to show. If you want to add a bond
> between two atoms, you can do this interactively using the Mouse menu
> item for adding/removing bonds, by loading a PSF file as others have
> mentioned, or by using molefacture or other tools to edit your
> structure and produce a PSF if you don't have one already.
> Preparing an image is easy, and is done using the File->Render menu
> item, where you can use the "snapshot" rendering method to do a
> capture of what's shown on the display.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Jan 09, 2008 at 10:23:31AM -0600, snoze pa wrote:
> > Thanks for ur mail but I am trying to generate a picture(graphics in
> png/tif
> > format) from VMD where two atoms are linked . How can I show in graphics
> > that the two atoms are linked.
> >
> > thanks
> >
> > On Jan 9, 2008 7:39 AM, Nazanin Samadi <nsamadi_at_gmail.com> wrote:
> >
> > >
> > > Hi, what do you mean by link? if you mean you want to have a bond
> between
> > > atoms you should use the psf file format for atoms coordinates. you
> can not
> > > do that by xyz file. actually there is another way too, but I do not
> > > recommend.
> > > I hope this was your question.
> > >
> > > nazanin
> > >
>
> --
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>