nonstandard RNA residues missing rungs

[Elaine Meng]

Modified RNA residues in structures such as 1ehz are missing "rung" pseudobonds. However, at least all the nonstandard bases I looked at were clearly identifiable as either purine- or pyrimidine-derived. I don't know if mmCIF has something like the PDB-format MODRES that reveals this, but the "easy" way to tell if they are already known to be in a nucleic acid chain is by the last letter of the residue name. For example, 2MG is derived from G. In 1ehz:

purine-derived (use N1): 2MG OMG M2G YYG 7MG 1MA
pyrimidine-derived (use N3): H2U OMC PSU 5MC 5MU

I realize "rungs" is somewhat experimental so you may not want to spend time improving it in this way. Just thought it would be good to record this information somewhere. The related problem with ribbons in general #402 is certainly worse.

[Tom Goddard]

Fixed.

Rungs now shown for non-standard nucleic acids. The rungs command no longer restricts to particular residue names. If a residue has a C3' atom then it tries to draw a rung to N1 or N3. It chooses N1 or N3 based on whether the residue as a C8 atom, which is present in purines but not pyrimidines.