show nucleotide representations for modified nucleic acids

[Elaine Meng]

Doesn’t the mmCIF file or some lookup table available from wwPDB say what is the unmodified version of the modified base?

Looks like any modified base (nonstandard nucleic acid residue) is shown as all atoms and ignored by "nucleotides". If there is knowledge of the corresponding unmodified type, consider having "nucleotides" (including initial display) attempt to show it in the same way as would be used for the unmodified base instead. Lots of nonstandard nucleic acids are just hydroxylated and methylated variations of a standard residue. If the required atom(s) aren't there, it could fail back to all atoms for that residue.

Similarly, could also apply the nucleic coloring, or perhaps a slightly modified (e.g. lighter or darker than for the unmodified residue) version of the nucleic coloring.

[Greg Couch]

Looking at 1h0q, the modified nucleic acids, that are based on standard amino acids, are depicted abstractly. But the color isn't changed. How important is that?