There seems to be an issue with "jed flip" ing a residue which one has split into an alternate conformer. Simple to reproduce ("Get monomer" (NUT) -> Make alternate conformation->Jed-flip). At first I hoped it was just because we were not adding the alternate conformer ID into the atom CID given to the command, but I have now pushed a change that addresses that scenario, and the atom spec now includes the alternate conf
There seems to be an issue with "jed flip" ing a residue which one has split into an alternate conformer. Simple to reproduce ("Get monomer" (NUT) -> Make alternate conformation->Jed-flip). At first I hoped it was just because we were not adding the alternate conformer ID into the atom CID given to the command, but I have now pushed a change that addresses that scenario, and the atom spec now includes the alternate conf