From: DanLiu (
Date: Mon Apr 15 2013 - 11:32:58 CDT

Hi John,
Thanks a lot, I know how it works now.
Best wishes
On Apr 15, 2013, at 5:11 PM, John Stone wrote:

> Hi,
> 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.
> Cheers,
> 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