VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 09 2008 - 22:51:46 CST

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
> > 

-- 
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