Dear Stephen,
The thought that using the CSD via Mogul for generating good refinement
dictionaries in the first place was THE way to go, rather than relying on
the PDB to use the same information later to try and catch errors at the
time of deposition, has been the driving force in the development of Grade
by Oliver Smart and Thomas Womack at Global Phasing, thanks to a very
fruitful interaction with the CCDC.
Grade generates restraints using Mogul for data mining CSD structures.
Where this data mining does not provide sufficient information, quantum
chemical methods are used. Grade produces restraints not only on bond
lengths and bond angles, but also on planarity and on torsion angles. To get
the best restraints, access to Mogul is required; but if you do not have
access to it, you can run it via the command "grade -nomogul". More
information can be found on the following page of the BUSTER Wiki:
http://www.globalphasing.com/buster/wiki/index.cgi?BusterLigandRestraints
and, through the "grade" hyperlink on that page or directly, at
http://www.globalphasing.com/buster/wiki/index.cgi?GradeMainPage
Oliver Smart covered Grade in his talk at last year's CCP4 Study Weekend.
Grade was released to our beta users on 8 October 2010 and to academics
as part of the BUSTER release on 20 July 2011. The latter is available free
of charge via the BUSTER homepage at
http://www.globalphasing.com/buster/
Any users whom Colin Groom would enable to connect to their nearest CSD
installation would immediately be able to use Grade's full capabilities. I
would recommend that anyone seriously interested in ligand stereochemistry
should take up Colin's offer.
I should add that, with the kind and gratefully acknowledged permission
of the CCDC, we are currently working on a Web server version of Grade for
use by academics.
With best wishes,
Gerard.
--
On Tue, Jan 10, 2012 at 10:23:02AM +0000, Stephen Graham wrote:
> "...available to anyone who has access to the Cambridge Structural
> Database System"
>
> How many academic labs will bother / can afford to buy a CCSD license
> just to check the geometry of small molecule ligands, especially when
> they need to do so them only once every blue moon?
>
> The ability for the PDB to check a ligand against the CCSD upon
> deposition would be great. The ability to generate the restraint
> definition for free via the web before deposition is better: that's
> why people use PRODRG!
>
> Stephen
>
> On 10 January 2012 09:50, John Liebeschuetz <j...@ccdc.cam.ac.uk> wrote:
> > On 9 January 2012 06:13, Shveta Bisht <shv...@mbu.iisc.ernet.in> wrote:
> >> Dear all
> >>
> >> I have generated a refmac cif file for a molecule using PRODRG. I used
> >> JME editor to draw the molecule and ran PRODRG online with the
> >> options: Chirality-Yes, Charges-Reduced and EM-Yes. Please check the
> >> attachments for the molecule drawing and the expected bond lengths as
> >> listed in the PRODRG generated cif file. There are some unusual
> >> values. I have listed them below along with the likely explanations
> >> (just guesses).
> >>
> >> DRG CAR CAK single 1.390 0.025 DRG CAQ
> >> CAB single 1.390 0.025 DRG CAT CAI single
> >> 1.390 0.020 All three are C-C single bonds where one of the carbons
> >> belong to aromatic ring. This might lead to a short bond, although
> >> 1.39 seems to be too short for this.
> >>
> >> DRG CAI NAL double 1.340 0.022 DRG CAP
> >> NAL single 1.340 0.022 Here N and both the carbons are
> >> sp2 hybridization, so there can be delocalization of electrons. Thus
> >> both bonds (single and double) are of similar length.
> >>
> >> DRG CAP CAA double 1.530 0.025 As mentioned
> >> above, if pi (unhybridized) electrons of CAP are involved in CAP NAL
> >> bonding, then CAP CAA double bond essentially becomes a single bond
> >> with 1.53 bond length.
> >>
> >> I need advise on the way I have run prodrg and the explanations for the
> >> results.
> >> Is it common to observe such values? Or it is due to the alternating
> >> single and double bonds in this structure.
> >
> > Dear Shveta,
> >
> > I'd like to follow up Ian Tickle's answer. A survey we carried out
> > recently suggested that up to 70% of ligand structures in the PDB had bond
> > and bond angle errors that could have been removed by better choice of
> > restraints (to be published). Although most of the errors found are small,
> > some were very large (> 10 s.d. from mean).
> >
> > The Mogul program (http://www.ccdc.cam.ac.uk/products/csd_system/mogul/)
> > can be used to analyse the geometry of any feature in a 3D ligand model
> > against data in the Cambridge Structural Database and is available to
> > anyone who has access to the Cambridge Structural Database System. The
> > GRADE dictionary generation software from Global Phasing uses Mogul
> > information behind the scenes to generate bond and bond angle restraints.
> > In addition ligand validation and restraint correction using Mogul will
> > become available via COOT before too long. Finally you might like to know
> > we are working with the PDB so that the geometry of ligand models can be
> > validated on submission.
> >
> > Regards
> > John
> >
> > Dr John W. Liebeschuetz
> > Research & Applications Manager
> > Cambridge Crystallographic Data Centre
> > 12 Union Rd., Cambridge CB2 1EZ, UK
> > T: +44-(0)1223-762532
> > F: +44-(0)1223-336033
> >
> >
> >
> > LEGAL NOTICE
> > Unless expressly stated otherwise, information contained in this
> > message is confidential. If this message is not intended for you,
> > please inform postmas...@ccdc.cam.ac.uk and delete the message.
> > The Cambridge Crystallographic Data Centre is a company Limited
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> > Registered in England No. 2155347 Registered Charity No. 800579
> > Registered office 12 Union Road, Cambridge CB2 1EZ.
>
>
>
> --
> Dr Stephen Graham
> 1851 Research Fellow
> Cambridge Institute for Medical Research
> Wellcome Trust/MRC Building
> Addenbrooke's Hospital, Hills Road
> Cambridge, CB2 0XY, UK
> Phone: +44 1223 762 638
--
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