Dear Shawn, hello to Rutgers!
dnatco.datmos.org reports local conformers in terms of *much extended* A/B/Z concept. The conformers are called NtC classes and can be generalized into a high-level structural alphabet CANA. NtC classes are defined for dinucleotide blocks because to catch conformational diversity of NA you have to describe what's going on at the phosphodiester linkage. O3'-P-O5' bonds in context of sugar above and below. If interested, you can read doi:10.1093/nar/gkaa383.
To call the whole duplex A or B form is dangerous, look at "prototypical B-form" dodecamer 1bna. Widths of minor and major grooves are in my opinion extremely complicated phenomena. Their simple interpretation as distances between some atoms across the strand make perhaps sense in a narrow context of anti-parallel duplex held together by canonical (aka Watson-Crick) base pairs.
Hope it helps, Bohdan, bs.structbio.org On 2024-12-27 0:46, Shawn R wrote:
Dear Colleagues, I am trying to characterize nucleic acid duplexes with parameters such as minor/major groove widths, helix diameter and length, A and B form, etc. I am wondering if there is software that does all of these things. I've used x3DNA and DSSR, but they don't provide all of the descriptors I am looking for (though they are both wonderful and have been very useful). Many publications I've seen use CURVES+, but as far as I can tell, that server has not been available in a number of years. Manually measuring all of these parameters would take too much time over 10s of structures, unless such information is described easily in ChimeraX/PyMol/Coot/MOE that I am not aware of. Thanks for any insights! Shawn
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