Update chain description from fasta file
Hi, I really like the 'sequence update' feature that was introduced in Chimerax 1.9. I was wondering if it is possible to expand the capability of this command to update the sequence description/ sequence name from the header line of an opened alignment or fasta file and write it out with the cif file. It seems like currently the full sequence is updated from an associated fasta file but the sequence names are being ignored. Could the sequence name written into the ' entity.pdbx_description' column in the resulting cif file? Or maybe there is already an option that I missed? Also, as a secondary feature request, maybe the sequence update command could not only write the ' entity_poly.pabx_seq_one_letter_code_can' table but also use the available coordinates and residue names of the structure to write the '_entity_ poly.pdbx_seq,_one_letter_ code' table for each polymer that includes modified residues/ligands etc in parentheses in addition to the canonical one letter code where known. I could imagine that these capabilities would make depositing coordinates of macromolecular complexes with many chains to the PDB much easier and more interactive, so maybe this would be helpful for other people as well. Thank you to the Chimerax team & contributors for creating such a great program, Paul
Hi Paul, Although not exactly the same as what you're requesting, in recent daily builds you can enter a new name for a sequence by using the Sequence Viewer context menu (choose Edit... Rename Sequence) or the "sequence rename" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#rename> However, that is the name that is shown in the Sequence Viewer window, and is not the same as the longer description that is shown when you mouse over the chain in the 3D window, and is not written into saved mmCIF. You can also manually change the longer chain description (which would go into a saved mmCIF) using the "setattr" command to change the chain attribute "description" ... for example: setattr #1/A chain description "this is my NEW description for chain A" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2025, at 1:13 PM, Paul Sauer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I really like the 'sequence update' feature that was introduced in Chimerax 1.9. I was wondering if it is possible to expand the capability of this command to update the sequence description/ sequence name from the header line of an opened alignment or fasta file and write it out with the cif file. It seems like currently the full sequence is updated from an associated fasta file but the sequence names are being ignored. Could the sequence name written into the ' entity.pdbx_description' column in the resulting cif file? Or maybe there is already an option that I missed?
Also, as a secondary feature request, maybe the sequence update command could not only write the ' entity_poly.pabx_seq_one_letter_code_can' table but also use the available coordinates and residue names of the structure to write the '_entity_ poly.pdbx_seq,_one_letter_ code' table for each polymer that includes modified residues/ligands etc in parentheses in addition to the canonical one letter code where known.
I could imagine that these capabilities would make depositing coordinates of macromolecular complexes with many chains to the PDB much easier and more interactive, so maybe this would be helpful for other people as well.
Thank you to the Chimerax team & contributors for creating such a great program,
Paul
Thank you Elaine, setting the chain description attribute is something I hadn't thought about! Much appreciated Paul On Fri, Feb 21, 2025, 13:43 Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Paul, Although not exactly the same as what you're requesting, in recent daily builds you can enter a new name for a sequence by using the Sequence Viewer context menu (choose Edit... Rename Sequence) or the "sequence rename" command.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sequence.html#rename>
However, that is the name that is shown in the Sequence Viewer window, and is not the same as the longer description that is shown when you mouse over the chain in the 3D window, and is not written into saved mmCIF.
You can also manually change the longer chain description (which would go into a saved mmCIF) using the "setattr" command to change the chain attribute "description" ... for example:
setattr #1/A chain description "this is my NEW description for chain A"
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/setattr.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 21, 2025, at 1:13 PM, Paul Sauer via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I really like the 'sequence update' feature that was introduced in Chimerax 1.9. I was wondering if it is possible to expand the capability of this command to update the sequence description/ sequence name from the header line of an opened alignment or fasta file and write it out with the cif file. It seems like currently the full sequence is updated from an associated fasta file but the sequence names are being ignored. Could the sequence name written into the ' entity.pdbx_description' column in the resulting cif file? Or maybe there is already an option that I missed?
Also, as a secondary feature request, maybe the sequence update command could not only write the ' entity_poly.pabx_seq_one_letter_code_can' table but also use the available coordinates and residue names of the structure to write the '_entity_ poly.pdbx_seq,_one_letter_ code' table for each polymer that includes modified residues/ligands etc in parentheses in addition to the canonical one letter code where known.
I could imagine that these capabilities would make depositing coordinates of macromolecular complexes with many chains to the PDB much easier and more interactive, so maybe this would be helpful for other people as well.
Thank you to the Chimerax team & contributors for creating such a great program,
Paul
participants (2)
-
Elaine Meng -
Paul Sauer