6pkv connectivity

[pett]

In entry 6pkv, the mmCIF makes some missing structure into covalent bonds instead of pseudobonds (e.g. /C UNK 1209 to ASP 1246). The PDB reader makes those into pseudobonds. Seems to be because of the UNK.

[Greg Couch]

It's a bug in the mmCIF file. The file says that those two residues are adjacent. The entity sequence numbers, label_seq_id, are 1207 and 1208, and the author sequence numbers, auth_seq_id, are 1209 and 1246.

[pett]

I typically report problematic entries to info@…. Then they will either fix it or tell you why it isn't in fact a bug.

[Tristan Croll]

I've been seeing a few of these lately - 6iqk and 6swy are other examples.

[pett]

So it seems like this is standard procedure, so you probably really should mail info@… and find out if there is other info in the mmCIF you should be using to get the gapping right.