[chimerax-users] Where is the renumber sequence tool in ChimeraX?

[Phan, Isabelle]

That’s exactly what I needed, thank you Eric!

Isabelle

> On May 16, 2022, at 4:57 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
> CAUTION: This email originated outside of this organization.
>
> Hi Isabelle,
> To answer your question directly, chain.existing_residues is all the residues in the chain with atomic coordinates, in chain order, and can be used like a list. So, to renumber the first 10 residues starting with -7:
>
> s.renumber_residues(chain.existing_residues[:10], -7)
>
> To renumber the next 28 residues starting with 35:
>
> s.renumber_residues(chain.existing_residues[10:38], 35)
>
> and so forth. However if all you want to do is subtract a certain amount from each residue number (e.g. 8, to change residue number 1 to -7 and so forth) then this is simpler:
>
> for chain in s.chains:
> if chain.chain_id == "A":
> for r in chain.existing_residues:
> r.number -= 8
>
> --Eric
>
>> On May 16, 2022, at 4:43 PM, Phan, Isabelle via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Thanks Eric, this is very helpful.
>> Is it possible to renumber only a selected stretch of residues? That way I could start from the last gap to the C-term and work my way up the chain.
>>
>> Isabelle
>>
>>> On May 16, 2022, at 1:53 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>>
>>> CAUTION: This email originated outside of this organization.
>>> 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 at 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,
>>>>
>>>> Isabelle
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>>
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