From: John Stone (
Date: Mon Apr 15 2013 - 10:11:28 CDT

  In order to see the bonds that you're adding and deleting,
first, make sure you're using a graphical representation that
actually shows bonds. Once you've check that, then you should
be able to click pairs of target atoms and see bonds added or
deleted as you go. You will indeed see text labels added to the
atoms you've selected as a form of visual confirmation of the
atoms you're selecting before the bond is added or deleted.
You can make the labels go away when you're done using the
Labels Window found in VMD Main|Graphics|Labels.

Once you've added/deleted bonds, you will (presumably) want to save
your modified structure. Be sure to store the updated structure to
a file format that stores bonds explicitly (e.g. PSF) so that when you
load it back in your changes aren't lost.

  John Stone

On Mon, Apr 15, 2013 at 02:04:24PM +0200, DanLiu wrote:
> Dear All,
> I'm trying to remove and add bonds among atoms, but after clicking target atoms, nothing expected happens, just a label shows up. Whoever knows what else should I do?
> Thank you.
> Best
> Dan

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349