[chimerax-users] change chain ID

[Eric Pettersen]

Hi Ben,
	Yes I am aware that recent versions of Modeller can take mmCIF files as input, which allows for multi-character chain IDs.  When I started writing the Modeller support in ChimeraX, ChimeraX had no ability to save mmCIF files, so PDB files were used.
	On my very long to-do list is revamping the Modeller support to use mmCIF files to get around the single-chain-ID limitation, but it isn't very high on the priority list since the rename-chain workaround exists.  I also have little idea how much effort is involved, since I don't know how well ChimeraX's mmCIF output will correspond to what to what Modeller wants.  For instance, the PDB code had to be revised to allow non-standard residues to be written as ATOM records instead of HETATM records if they were part of the sequence being modeled.  Things like that are probably lurking around if the code switches to mmCIF.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Oct 26, 2020, at 5:38 PM, Ben Webb <ben at salilab.org> wrote:
> 
> I don't want to muddy the waters too much here, but Modeller itself shouldn't have any issues with templates with multi-character chain IDs. But perhaps ChimeraX is giving Modeller PDB files (in which case you'd be limited by the PDB format to 1 character)? Modeller *should* be able to take mmCIF files as templates, which wouldn't be limited.
> 
> 	Ben
> 
> On 10/26/20 3:29 PM, Elaine Meng wrote:
>> Hi Tiglath,
>> That message means exactly what it says: Modeller cannot handle templates with multi-character chain IDs.
>> I see that when you use
>> open pdbe_bio:3r2p
>> ... then you get one chain A and one chain AA (two characters, = multi-character, so can't be used as Modeller template).  This is shown in the Log when you open the structure.  Not sure why PDBe chose to name the second chain as AA, but you can change it to a single character instead, for example to B with "setattr":
>> setattr /AA chain chain_id B
>> Sometimes (but not in this case) you might need two commands to change the chain ID instead of one, as explained in this recent post:
>> <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2020-October/001565.html>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>> On Oct 26, 2020, at 3:02 PM, Moradkhan, Tiglath A <tmoradkhan at csus.edu> wrote:
>>> 
>>> Hi Elaine
>>> OK. Thank you for the help. I have one more question. So I'm building a C-terminal dimer model of human Apo A-I using 3R2P as a template model (a C-terminal truncated x-ray crystal structure of the protein). I loaded the biological assembly (a dimer) in ChimeraX and used the Sequence viewer to get the template-query alignment. But when I try to run Modeller, it gives me the following message: "Modeller cannot handle templates with multi-character chain IDs". Am I missing something here?
>>> I would be very grateful for your help.
>>> Thanks
>>> Tiglath
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> 
> -- 
> ben at salilab.org                      https://salilab.org/~ben/
> "It is a capital mistake to theorize before one has data."
> 	- Sir Arthur Conan Doyle
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