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Hi Alex Essentially what it's saying is that it has found a systematic discrepancy between the bond lengths computed from the PDB co-ordinates and its own internal 'standard' dictionary bond length values. One way of resolving this discrepancy is by rescaling the unit cell: in your example the cell has to be made smaller in all directions by the factors given relative to the unit cell determined from the assumed X-ray wavelength & crystal-detector distance and the dimensions of the diffraction pattern. See http://swift.cmbi.ru.nl/gv/pdbreport/checkhelp/104l/index.html#28 (note the example given there illustrates the opposite case where the unit cell has to be made larger). Because the X-ray intensities are principally determined by the fractional co-ords, this implies that WhatCheck believes it's necessary to shrink the PDB structure, and hence all the inter-atomic distances, by the same factors, thereby making it fit into the slightly smaller unit cell, in order to get agreement with the dictionary bond lengths. Hence as you say the PDB structure appears to be dilated (stretched), and the bond lengths based on the refined PDB co-ords will be systematically longer than the dictionary values. The WhatCheck document above cites a number of possible explanations of this phenomenon, quote: "First the cell used in refinement can be different from the best cell calculated. Second, the value of lambda used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.". Others have suggested possible discrepancies between the dictionary values used by WhatCheck and those used by the refinement programs: this is indeed a possibility & needs to be checked. For older structures it's quite likely that the precise set of dictionary values used will not have been recorded anywhere, making checking impossible! Zbyszek Dauter did a limited survey of a few high res structures a while back (JMB 1998, 276, 417-436, see pp 423-5) and concluded that in all cases of synchrotron data, wavelength and/or crystal detector distance miscalibration was to blame (diffractometer data didn't suffer from this effect), but I'm not aware of more recent surveys. For structures say > 5 years old I think wavelength/distance miscalibration is the most likely explanation, however for the majority of recent structures I think it's much less likely. Assuming that any discrepancies in the dictionary values are found not to be significant, my own view is that for recently collected data the experimentally determined cell should be left well alone, and that anisotropy of the thermal motion is the most likely explanation. X-ray diffraction measures the time- & space-averaged structure which will have slightly shorter average bond lengths than the theoretical static structure. The "libration correction" which can easily amount to several percent is routinely applied in small molecule structure determinations, but very unusual in MX determinations (for one thing it requires a TLS model of the anisotropic motion at the side-chain level); hence we're not comparing like with like. Note that the correct way of dealing with the libration correction is to correct the target distances in the dictionary on a case-by-case basis: the co-ordinates themselves are not affected by this. The libration effect will increase with increasing overall B factor & it would be interesting to see if there's any correlation between the overall cell scaling factor determined by WhatCheck and the overall B factor. Cheers -- Ian > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On > Behalf Of Alex Gutteridge > Sent: 22 November 2005 09:28 > To: [email protected] > Subject: [ccp4bb]: WHATCHECK Deformation Matrix > > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Hi, > > I'm using WHATCHECK > (http://swift.cmbi.ru.nl/gv/pdbreport/) to scan some crystal > structures for unit cell scaling problems. I'm doing this > because the analysis I want to do on these structures will be > sensitive to these kind of errors. At this point I should > mention that I'm not a crystallographer by trade, so forgive > me if this is an obvious/stupid question. WHATCHECK gives a > 'deformation matrix' as part of it's output in this section. > Am I right in thinking that if the matrix looks like this > (from PDB code 2DHB): > > 0.987651 -0.000042 -0.000855 > > -0.000042 0.985582 -0.000365 > > -0.000855 -0.000365 0.987811 > > Then it is (essentially saying) the structure as given in the > PDB file is stretched about 1-2% (scale factor of 0.99-0.98) > along each axis? And so any measurement of length/distance in > the structure will be 1-2% longer than it should be? Also > does anyone know of a program that can apply this matrix to a > PDB file to get the correctly scaled structure. I've found > one paper that implies they did this, but they don't really > say how. Thanks in advance! > > > Alex Gutteridge > > EBI > Wellcome Trust Genome Campus > Hinxton > Cambs CB10 1SD > UK > > Tel: 01223 492546 > Email: [EMAIL PROTECTED] > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. 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