On Thursday, 12 June, 2014 20:24:43 Joel Tyndall wrote:
> 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.
As of January 2014 this is indeed being done as part of the PDB deposition
process.
Anyone who has deposited a structure containing a ligand this year has
probably been surprised, pleasantly or otherwise, by the table of geometry
violations/ouliers for each ligand.
If you missed the various announcements, you may wish to try it out on
your own structures here:
http://wwpdb-validation.wwpdb.org/validservice/
> I also believe that cif file generation can be improved.
Indeed. All of the library-generation tools I am aware of are flawed in
their own idiosyncratic ways. I think I shall start a campaign to treat
errors in the cif libraries as "bugs", and encourage people to report
these bugs in the libraries we all use just as they do for bugs in the
programs we all use.
Ethan
> 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim
> Gruene
> Sent: Friday, 13 June 2014 5:54 a.m.
> To: CCP4BB@JISCMAIL.AC.UK
> 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 <t...@shelx.uni-ac.gwdg.de>
> > 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
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
