[Chimera-users] Assigning nucleotide representation to non-canonical nucleotides

[Greg Couch]

ChimeraX is slightly better than Chimera for nucleotides.  For example, 
selecting the slab and tube elements select the corresponding atoms.  
And non-standard nucleotides are recognized for ladders.  It is also faster.

For non-standard nucleotides to be recognized as such, that needs to be 
annotated.  In a PDB file, that means the base residue needs to listed 
in a MODRES record.  And for a mmCIF file, the CCD entry it needs to be 
listed in the chem_comp.mon_nstd_parent_comp_id item.  I see that the 
PDB added a pdbx_struct_mod_residue mmCIF table that directly 
corresponds to the PDB file's MODRES record. ChimeraX does not yet 
support that -- I'll make a ticket for that.  Let me know if you want to 
know when it is implemented.

     -- Greg

On 5/14/2022 3:36 AM, Jérôme Rihon via Chimera-users wrote:
> Dear dr. Meng,
>
> Thank you for the fast reply.
>
> The nucleobases present in the XNA I'm researching contains standard purines and pyrimidines. It is the sugar moiety that has been altered quite dramatically. The nucleobase is attached to a C1' , but its residue is recognised as non-standard by Chimera (MA, MC, MG, MT) . The residues all follow the standard AMBER Tree Structure (M,B,S,E ..) ordering. (my apologies, I should have been more clear about this in the first email).
>
> I am trying through the command line, in Chimera, but it will not recognise the nucleotides as a nucleotide object.
>
> One way to `cheese` the depiction is by changing the name of the residues to A,C,G,T and then it will recognise then as standard nucleotides and will depict them as slabs, though the connectivity of the sugar is all off, which that is to be expected. Using the tube/slab depiction sweeps this under the rug.
>
> I'll be trying one of these methods.
>
> Thanks again for the help!
>
>
> Kind regards,
> ________________________________________
> Van: Elaine Meng <meng at cgl.ucsf.edu>
> Verzonden: vrijdag 13 mei 2022 17:14
> Aan: Jérôme Rihon
> CC: chimera-users at cgl.ucsf.edu
> Onderwerp: Re: [Chimera-users] Assigning nucleotide representation to non-canonical nucleotides
>
> Dear Jérôme,
> The slabs are drawn based on the presence of atom names that appear in standard purine and pyrimidine nucleotides.  It might work for nonstandard ones that contain those atoms, but in general, if the base is different enough that it does not contain those atom names, the slab is not drawn.
>
> I know that the Nucleotides tool can draw ladders, slabs, etc. for the standard bases + pseudouridine.  If you try using it on other bases and it keeps showing sticks only, then my guess is no, it does not work for those.
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/nucleotides/nucleotides.html>
>
> Also, as far as I know, the base recognition in ChimeraX for drawing nucleotides is the same as in Chimera.
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/nucleotides.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 May 13, 2022, at 2:21 AM, Jérôme Rihon via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>
>> Dear
>>
>> I was wondering if there is a way to represent non-canonical (otherwise known as xenobiotic) nucleic acids through UCSF Chimera (specifically, not ChimeraX .. haven't made the jump yet).
>> I've looked through your documentation on the `nucleotides` section but was not able to find something along those lines. My PI told me it was possible, but I can't seem to find it.
>> My apologies if I should be looking for this function elsewhere, but I thought it'd be easier to just ask.
>>
>> Many thanks in advance!
>>
>> Kind regards,
>> Met vriendelijke groeten,
>> Cordialement,
>> ______________________
>> Rihon Jérôme
>> jerome.rihon at kuleuven.be | +32 16 32 53 57
>> PhD researcher @Rega Institute for Medical Research | Laboratory of Medicinal Chemistry | Computational Research
>> Herestraat 49 - box 1041, 3000 Leuven
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