OK thanks Eric. 
Kai
From: Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Tuesday, September 24, 2024 1:35 PM
To: Kai Cai <Kai.Cai@UTSouthwestern.edu>
Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Re: Bond built manually with ChimeraX not shown up in Coot
 
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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