.and there is always the twilight collection and the gems shown in the associated paper:
http://www.ruppweb.org/twilight/default.htm Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Alessandro Nascimento Sent: Donnerstag, 17. Oktober 2013 23:22 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Problematic PDBs Hi Lucas, this book (http://www.amazon.com/Structural-Bioinformatics-Methods-Biochemical-Analysi s/dp/0471201995/ref=sr_1_2?s=books <http://www.amazon.com/Structural-Bioinformatics-Methods-Biochemical-Analysi s/dp/0471201995/ref=sr_1_2?s=books&ie=UTF8&qid=1382044405&sr=1-2&keywords=st ructural+bioinformatics> &ie=UTF8&qid=1382044405&sr=1-2&keywords=structural+bioinformatics) brings nice examples of protein structures with "unusual features" in the structure validation chapter . I used it on my "protein modeling"course and it is definitely worth buying. I small list taken from the book (unless I am very much mistaken) includes these structures: 1. 2ABX 2. 1GMA 3. 1CYC 4. 3PGM 5. 1CTX 6. 2GN5 7. 2ATC 8. 1PYP 9. 4RCR 10. 1TRC HTH, --asn [ ]s --alessandro 2013/10/17 Lucas <lucasbleic...@gmail.com> 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
