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>