Hello, just for the sake of completeness: this paper lists a bunch of known pathologies (I would not be surprised if they've been remediated by now):
http://www.phenix-online.org/papers/he5476_reprint.pdf Pavel On Thu, Oct 17, 2013 at 6:51 AM, Lucas <lucasbleic...@gmail.com> wrote: > Dear all, > > I've been lecturing in a structural bioinformatics course where graduate > students (always consisting of people without crystallography background to > that point) are expected to understand the basics on how x-ray structures > are obtained, so that they know what they are using in their bioinformatics > projects. Practices include letting them manually build a segment from an > excellent map and also using Coot to check problems in not so good > structures. > > I wonder if there's a list of problematic structures somewhere that I > could use for that practice? Apart from a few ones I'm aware of because of > (bad) publicity, what I usually do is an advanced search on PDB for entries > with poor resolution and bound ligands, then checking then manually, > hopefully finding some examples of creative map interpretation. But it > would be nice to have specific examples for each thing that can go wrong in > a PDB construction. > > Best regards, > Lucas >
