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

[Eric Pettersen]

Happy to help!

--Eric

> On May 16, 2022, at 5:25 PM, Phan, Isabelle via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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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