Hi Kai,
If the CONECT record indicating that those two atoms are bonded is in the PDB file then this is a problem with Coot -- you would need to ask on the Coot mailing list why it isn't showing that bond.

--Eric

On Sep 24, 2024, at 11:29 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Eric, 

Thanks for the reply. I tried both cif and pdb, neither seems to work for me. I can see the connection has been created when I inspected pdb file, but somehow the bond is not present when opened in Coot. 

Thanks,
Kai
From: Eric Pettersen <pett@cgl.ucsf.edu>
Sent: Tuesday, September 24, 2024 1:02 PM
To: Kai Cai <Kai.Cai@UTSouthwestern.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Bond built manually with ChimeraX not shown up in Coot
 

EXTERNAL MAIL

Hi Kai,
Did you write the file as PDB or mmCIF when you saved it from ChimeraX?  When I use Build Structure to join a NAG to an ASN, the resulting PDB file has the proper LINK/CONECT records.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Sep 24, 2024, at 9:51 AM, Kai Cai via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear colleagues,

I am trying to build a N-glycan into my model using 'bond' command with ChimeraX, by connecting the ND2 atom from an ASN residue to the C1 atom of the N-glycan (NAG). However, the manually built bond didn't show up when I opened the coordinates in Coot. Is there a way to overcome this issue? The bond length is 1.4 Å. Thanks in advance! 

Cheers,
Kai

UT Southwestern
Medical Center
The future of medicine, today.
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