Hi Isabelle, Yes, there is no user-friendly way to renumber residues in ChimeraX yet. The renumber_residues() method that you found can do it, if you know how to call it correctly. Here is some code to renumber chain A in a structure starting from -7: from chimerax.core.commands import run s = run(session, "open my_structure_file")[0] for chain in s.chains: if chain.chain_id == "A": s.renumber_residues(chain.existing_residues, -7) The caveat is that if the chain has any missing residues, this renumbering won't maintain any jumps in numbering across those gaps -- the numbering will simply be consecutive. You would need fancier code to maintain jumps in numbering. --Eric Eric Pettersen UCSF Computer Graphics Lab
On May 13, 2022, at 2:56 PM, Phan, Isabelle via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
The sequence of my structure includes a tag and I want to renumber from -7 so that the first residue is the start Met. I tried the old chimera command resrenumber = FAIL. I googled and searched the docs, read the list of commands one by one, and still could not figure it out.
The API has a renumber_sequence() function but I don't understand the description (what’s "the given residues”? The chain?) and was unable to find an example on how to call this from the interface. I opened the python shell and typed:
from chimerax.core.commands import run run(renumber_residues('#1/A:*', -7)) # FAIL
Sorry if this is trivial, I am still completely baffled by ChimeraX despite using it for years.
Thanks,
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