Thanks Colin! I was also going to mention the Chemical Database Service, available to UK academics.
Their website is http://cds.dl.ac.uk/ In fact, the very nice and friendly CDS guys are just across the corridor from me, so please let me know if you have problems/questions. Cheers Martyn On Tue, 2012-01-10 at 12:53 +0000, Colin Groom wrote: > I'm sad to think that scientists may not 'bother' to use the CSD > system 'just' to check the geometry of small molecule ligands, as they > may, of course, be the main focus of the study, or the focus of > subsequent researchers who use the structures. Moreover, comparison of > small molecule and protein-bound ligand structures can be most > revealing. > > In answer to your question of access, the vast majority of research > universities in the world (with a chemistry department) already have > access to the CSD. In fact it is available in 72 counties, to > scientists in around 1,500 institutions. The problem you highlight is > that it's quite common for scientists not to realise that another > department, or their institutions library, already provide access to > the CSD system. I'll reply to any off-board emails should folks want > to know who their local contact is. > > In terms of affordability, the CSD system is maintained by the > Cambridge Crystallographic Data Centre, which is a non-profit, > charitable organisation. It is available at below cost to academics. > Anyone who genuinely cannot afford the modest charge, which is used > for the ongoing funding of the CSD, is of course given free access. > The CSD and other chemistry databases are also freely available to UK > researchers through the excellent (EPSRC funded) Chemical Database > Service operated from Daresbury. > > You're right that the CCDC:PDB collaboration to develop on-line tools > check ligands and generate dictionaries 'is great'- and Gerard might > let us know how he's getting on? > > Colin > > Dr Colin R Groom > Email: gr...@ccdc.cam.ac.uk > Executive Director > Phone-direct: +44-(0)1223-336020 > Cambridge Crystallographic Data Centre > Phone-messages: +44-(0)1223-336408 > 12 Union > Road FAX: +44-(0)1223-336033 > Cambridge CB2 1EZ, UK Website: > http://www.ccdc.cam.ac.uk > > > > > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen > Graham > Sent: 10 January 2012 10:23 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] : Re: [ccp4bb] unusual bond lengths in PRODRG cif file > > "...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 > > by Guarantee and a Registered Charity. > > Registered in England No. 2155347 Registered Charity No. 800579 > > Registered office 12 Union Road, Cambridge CB2 1EZ. > > > -- *********************************************************************** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * * Fax: +44 1925 603634 Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***********************************************************************
