PDB coordinates missing--how to add residues to N-terminus
The first few N-terminus residues of a seq are grayed out in the PDB sequence viewer and are missing in the PDB chain. It is even possible for ChimeraX to make the peptide bonds to glue on the missing residues in the helix in accurate XYZ positions tacked on at N-terminus without resorting to generating an Alphafold model? I am also thinking ISOLDE won't work.
Hello, As to "accurate," that is always a judgment call... and those residues may be disordered/flexible anyway, which may be why they were not resolved in the PDB structure. Setting that aside, there are multiple possibilities of what to try other than running an AlphaFold prediction: (A) you can use ChimeraX search the Alphafold Database to see if the monomer of that sequence was already predicted (or perhaps a sequence that is almost the same), and if so, to fetch it. See the ChimeraX AlphaFold tooloptions for Fetch and Search, or the "alphafold" command "fetch" "match" and "search" subcommands: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#match> ...or the "alphafold" command "fetch" "match" and "search" subcommands: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html> (B) you can use the ChimeraX "Model Loops" tool (interface to Modeller) to add residues that are in the sequence but missing from the 3D structure. You can open that tool from the menu menu, Tools... Sequence... Model Loops, or from the Sequence Viewer window context menu,Tools... Model Loops <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html> (C) you can use the Build Structure tool, the Start Structure section, to build the peptide as a separate model with specified phi/psi backbone angles. You can then combine it with the rest of the protein using the Join Models section of Build Structure. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.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 Jul 12, 2023, at 5:36 PM, stevensb--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
The first few N-terminus residues of a seq are grayed out in the PDB sequence viewer and are missing in the PDB chain. It is even possible for ChimeraX to make the peptide bonds to glue on the missing residues in the helix in accurate XYZ positions tacked on at N-terminus without resorting to generating an Alphafold model? I am also thinking ISOLDE won't work.
Elaine, Thank you very much. Extremely helpful! Bruce R. Stevens, PhD | Professor Emeritus College of Medicine | University of Florida Email: stevensb@ufl.edu<mailto:stevensb@ufl.edu> ----------------------------------------------- From: Elaine Meng <meng@cgl.ucsf.edu> Date: Wednesday, July 12, 2023 at 8:58 PM To: Stevens,Bruce R <stevensb@ufl.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] PDB coordinates missing--how to add residues to N-terminus [External Email] Hello, As to "accurate," that is always a judgment call... and those residues may be disordered/flexible anyway, which may be why they were not resolved in the PDB structure. Setting that aside, there are multiple possibilities of what to try other than running an AlphaFold prediction: (A) you can use ChimeraX search the Alphafold Database to see if the monomer of that sequence was already predicted (or perhaps a sequence that is almost the same), and if so, to fetch it. See the ChimeraX AlphaFold tooloptions for Fetch and Search, or the "alphafold" command "fetch" "match" and "search" subcommands: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Falphafold.html%23match&data=05%7C01%7Cstevensb%40ufl.edu%7Ca3009bf38928468b784e08db833c4d35%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638248067249286366%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=zsqvgA7mJCw9twOyxALnt70UyqfQGVUPena%2FekNFkCc%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#match>> ...or the "alphafold" command "fetch" "match" and "search" subcommands: <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Falphafold.html&data=05%7C01%7Cstevensb%40ufl.edu%7Ca3009bf38928468b784e08db833c4d35%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638248067249286366%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=zKTn5EOFiuFOf%2FkCCswDLXeViFutkOkH7oYFIVlehEw%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html>> (B) you can use the ChimeraX "Model Loops" tool (interface to Modeller) to add residues that are in the sequence but missing from the 3D structure. You can open that tool from the menu menu, Tools... Sequence... Model Loops, or from the Sequence Viewer window context menu,Tools... Model Loops <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fmodelloops.html&data=05%7C01%7Cstevensb%40ufl.edu%7Ca3009bf38928468b784e08db833c4d35%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638248067249286366%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SdgHvf4OypQ3lJxiV3ai7yg%2BfHYH2TF4TvOqvp6Ogms%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelloops.html>> (C) you can use the Build Structure tool, the Start Structure section, to build the peptide as a separate model with specified phi/psi backbone angles. You can then combine it with the rest of the protein using the Join Models section of Build Structure. <https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fbuildstructure.html&data=05%7C01%7Cstevensb%40ufl.edu%7Ca3009bf38928468b784e08db833c4d35%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638248067249286366%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZYFD7A81D6Lph7uR9CnZqkkG7E8W8ibizPsq37mUANk%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.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 Jul 12, 2023, at 5:36 PM, stevensb--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
The first few N-terminus residues of a seq are grayed out in the PDB sequence viewer and are missing in the PDB chain. It is even possible for ChimeraX to make the peptide bonds to glue on the missing residues in the helix in accurate XYZ positions tacked on at N-terminus without resorting to generating an Alphafold model? I am also thinking ISOLDE won't work.
participants (3)
-
Elaine Meng -
Stevens,Bruce R -
stevensb＠ufl.edu