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

Elaine Meng meng at cgl.ucsf.edu
Fri May 13 08:14:51 PDT 2022

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.

Also, as far as I know, the base recognition in ChimeraX for drawing nucleotides is the same as in Chimera.

I hope this helps,
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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