Thanks a lot you Elaine. 

-------- Original message --------
From: Elaine Meng <meng@cgl.ucsf.edu>
Date: Thu, 1 Jun, 2023, 21:48
To: Aditi Laddha <laddhadi@iitk.ac.in>
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] missing bonds when visualizing in Chimera

Hi Aditi,
Without having that same PDB file to look at, I can only guess the cause (the picture only shows the result, not the cause): probably the file does not have explicit CONECT records and the distance between the atoms is longer than expected for a bond and Chimera does not guess the bond, whereas other programs guess there is a bond. 

In Chimera, you can just add the bond if you want, e.g. select the two atoms (Ctrl-click on one, Shift-Ctrl-click on the other) and use command:

bond sel

<https://www.rbvi.ucsf.edu/home/meng/docs/UsersGuide/midas/bond.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                      
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 1, 2023, at 12:21 AM, Aditi Laddha via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
>
> Hello Elaine,
>
> I am facing some difficulties visualizing my structure in Chimera; whenever I open the .pdb file containing the sucrose molecule, the bond between glucose and fructose is missing (glycosidic bond). But all bonds are visible when I open the same file in other programs.
>
> I want to know about its hydrogen bond interaction with my protein and visualize them in Chimera.
>
> Please help me with this issue.
> I am attaching an image of a sucrose molecule having a missing bond when visualized in Chimera.
>
> ---
> Regards,
> Aditi Laddha
> PhD Scholar
> Indian Institute of Technology,
> Kanpur, Uttar Pradesh 208016
> <Screenshot from 2023-06-01 12-47-00.png>