Hi Sam, Associating a chain to an alignment sequence doesn’t change ChimeraX’s opinion of what the chain's sequence is, since there are various reasons you might what to associate a chain to what might be only a similar sequence. Nonetheless, what you want to do is pretty useful, so I will try to add support for it in the sequence viewer sometime soonish. In the interim you can get what you want by running the attached script, which will transfer alignment sequences to each associated chain. You run the script simply by opening it (“open /where/you/saved/xfer-seq.py”). --Eric Eric Pettersen UCSF Computer Graphics Lab 
On Jun 10, 2024, at 3:05 AM, Samuel Haysom via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I would like to use a .fasta file that I have loaded into ChimeraX to update the SEQRES records of a PDB file that is also loaded into ChimeraX. Currently the loaded PDB file only has SEQRES records for the residues that are modelled, while the .fasta file has the full, sequence with no gaps. I have tried loading in the .fasta file and then using the $ sequence associate command to associate it with the relevant pdb chain. However, when I then save out the pdb file (using the $ save command) and then examine the pdb file it still only records the modelled residues. Is there any way to force the written pdb file to have the full sequence as uploaded in the .fasta file?
I am running chimeraX version 1.7 (2023-12-19).
Thanks for your help, Sam
Samuel Haysom <mailto:Samuel.Haysom@nxera.life> Research Scientist • Biophysics Nxera Pharma UK <https://nxera.life/> Limited
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