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 <mailto:pett@cgl.ucsf.edu>> Sent: Tuesday, September 24, 2024 1:02 PM To: Kai Cai <Kai.Cai@UTSouthwestern.edu <mailto:Kai.Cai@UTSouthwestern.edu>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto: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. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://urldefense.com/v3/__https://mail.cgl.ucsf.edu/mailman/archives/list/...> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.
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