Bond built manually with ChimeraX not shown up in Coot
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.
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/
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. _______________________________________________ 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/chimerax-users@cgl.ucsf.edu/__;!!MznTZTSvDXGV0Co!GhBejgZtRF2wvmYaEwxyNCD3-tgkZUbOE5Ob5kX2o3BabSH0StgM_ISZk53HZLIz2PJCi59AtBedDpUeJvu9se8D$> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying.
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.
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/
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<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/chimerax-users@cgl.ucsf.edu/__;!!MznTZTSvDXGV0Co!GhBejgZtRF2wvmYaEwxyNCD3-tgkZUbOE5Ob5kX2o3BabSH0StgM_ISZk53HZLIz2PJCi59AtBedDpUeJvu9se8D$> CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. _______________________________________________ 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/chimerax-users@cgl.ucsf.edu/__;!!MznTZTSvDXGV0Co!HuyflC8_AYKZQDunrSEl2fWcUPhmceJDeckvaylQSjPOdj3_gxmkTweUfqwTkFj_d0Q2en1L_FWIBQRkskwyLrJc3Q1kb2O3Lgu50w$>
participants (2)
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Eric Pettersen -
Kai Cai