Hi, I saw Jeffs post with interest and have held off until now. It is relatively easy to find structures with bad geometry for small molecules but it does not do any good simply pointing them out. What I believe is needed is a way to fix the problem. There are several possible ways. The pdb could parse new structures through a checking process to check the geometry of small molecules. This, I would presume, could be done via the CSD. I also believe that cif file generation can be improved. The developers of the available programs are doing a great job but as intelligent scientists we strive for perfection. I am unfortunately not in a position to develop software myself ( so maybe I should pipe down) but I would be happy to offer assistance (from my personal experience). In my experience I have had some issues with small molecule parametrisation ( or maybe I just deal with unusual molecules). By that I mean, on occasion I have had a .cif files that simply do not make sense or contradicts what you would expect in the geometry of a small molecule. I am aware of one "service" that does check against the CSD when generating cif files.
I read in one of the editorials, or related posts that one of the structures was corrected. This is also an option assuming the data has been deposited. My two cents J -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Tim Gruene Sent: Friday, 13 June 2014 5:54 a.m. To: [email protected] Subject: Re: [ccp4bb] Hosed-Up X-Ray Structures: A Big Problem Hi Jeff, there are quite a few implications in your brief email that each might open a long thread of discussion. As brief as possible I think one has to be a good scientist and a good crystallographier to fully understand the meaning of a crystal structure, and I think many people believe a crystal structure is just a set of coordinates. If someone tells me some distance in yards and I assume that's about the same as a meter I will surely get some dodgy results up to creating the first car accident on Mars ;-) Cheers, Tim On 06/12/2014 07:04 PM, Jeffrey Bell wrote: > Hi, Tim, > > Thanks for your comment. Do you agree with the editorial's claim that some > 25% of the deposited protein-ligand complexes might be dodgy in significant > details? > > > This editorial comment represents something that I often hear from drug > discovery professionals. Is it a matter of PR between crystallographers and > other scientists, or does a real problem exist? > > Cheers, > > Jeff Bell > PrimeX developer > Schrödinger, Inc. > > > On Tuesday, June 10, 2014 10:27 AM, Tim Gruene <[email protected]> > wrote: > > > > I hope that the contents of this section is obvious to most readers of > the ccp4 bulletin board. > > Cheer, > Tim > > > On 06/10/2014 03:40 PM, Jeffrey Bell wrote: >> An editorial comment about protein crystallography appeared under >> that title. It's short and worth considering. >> http://pipeline.corante.com/ > > > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
