Hi Tristan, Erroneous LINK records happen quite a lot and used to be the combination of aggressive annotation software and depositors not paying attention to the comments from the annotators. They make up a large fraction of the bug reports I have sent to the PDB over the years. They are usually fixed very quickly by the annotators, as long as someone takes time to report them.
This case looks like an error in a refinement program which nevertheless should have been caught by the depositors. What I would like to know is whether the deposited, pre-annotation model had the LINKs or not. LINKs are a bloody nightmare when it comes to annotation. At the moment there is no record keeping of targets and chemical modifications in a dictionary on the side of the PDB so there is also no standardisation. IMO mmCIF makes it easier to store the restraints with the coordinates, but there is still no neat mapping by LINK identfiers the way the LINKR format works in Refmac. I think that is a missed opportunity. Sorry for the rant, I blame the F1. Cheers, Robbie Op 11 nov. 2018 19:47 schreef Tristan Croll <ti...@cam.ac.uk>: I've seen instances like the following in roughly half a dozen deposited structures over the past year or so. Each time I've contacted the authors, who've been just as mystified as me by them - and certainly didn't add them on purpose. It seems to me that some fairly commonly-used package is erroneously turning clashes into LINK cards in some circumstances. I just found the following clearly wrong LINKs in 6caj (deposited January this year): LINK CD2 PHE I 266 CG2 THR I 272 1555 1555 1.47 LINK CE2 PHE I 266 CG2 THR I 272 1555 1555 1.47 ... which looks like the attached image. The same bonds are also specified in the mmCIF file, for the record. Anyone have any clue? Best regards, Tristan ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
