Dear Ian and Margriet, You are right, the correction needs to be done on F, not on |F|^2. If I recall correctly (I did not do it myself), the assumption was that Fobs = 0.5*Fobs(A) + 0.5*Fobs(B), so Fcorrected(A) = 2*Fobs - Fcalc(B) where A and B are the two orientations. Since one does not have an observed phase, one would have to take calculated phases. I am unsure though, if that was done in practise and one did not just subtract the absolute values. Since the inhibitor is usually only a small part of the total scattering mass, the phases might not differ too much and therefore the error would not be too big. In case of superposition of base pairs, I guess that the differences in scattering between the different base-pairs is not too much, so one might also be able to get away with not using phases, but here you are the expert.
Using this method, one could much better interpret the convoluted electron density, but one has to be very careful not introducing severe model bias. I would look in the literature in detail, what people from the HIV protease field had done to solve this problem. Cheers, Herman -----Original Message----- From: Ian Tickle [mailto:i.tic...@astex-therapeutics.com] Sent: Thursday, January 29, 2009 12:53 PM To: Schreuder, Herman R&D/DE; margriet.ova...@chem.kuleuven.be; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Small lines in diffraction pattern (more info) Hi Herman Aren't detwinning methods appropriate only in the case of true twin domains which are larger than the X-ray photon correlation length in order for the assumption to be valid that |F|^2 from each domain can be summed? This wouldn't give rise to the apparent 'diffuse scatter' phenomenon. However if what you are describing is rather static disorder of unit cells, which would give rise to diffuse scatter, where A & B type cells are randomly mixed (so a domain is only one or at most a few unit cells), as opposed to being confined to A & B type domains, then detwinning would not be appropriate. Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of > herman.schreu...@sanofi-aventis.com > Sent: 29 January 2009 11:19 > To: margriet.ova...@chem.kuleuven.be; CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] Small lines in diffraction pattern (more info) > > Dear Margriet, > > From your description and what James Holton wrote, it seems that you > have 2 types of unit cells: > A: with the "sense" strand in position 1 and the "antisense" > strand in position 2 > B: with the "antisense" strand in position 1 and the "sense" > strand in position 2 > If the crystal contacts are mainly via the backbone, your crystal may > contain a random distribution of both and the electron density you see > is a superposition of both and for the crystal packing, both chains > are identical. > > This situation is similar to the situation when an asymmetric > inhibitor is bound to a dimeric, symmetric molecule like e.g. > HIV protease. In this case, both orientations are deconvoluted using > detwinning methods for perfect twinning (see e.g. Proc Natl Acad Sci U > S A. 2002 November 12; 99(23): > 14664-14669). > The 34,34,34 cell is definitively too small, so I would process in the > 34,34,170 cell and detwin. You molecular replacement solutions should > tell you which twinning operator to use. > > Best regards, > Herman > > > > ________________________________ > > From: CCP4 bulletin board > [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Margriet Ovaere > Sent: Thursday, January 29, 2009 10:45 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Small lines in diffraction pattern (more info) > > > Dear all, > > > There were some comments about detector issues, but > these can be ruled out, to my opinion, since the lines > appeared on different beamlines. > > > Default settings of mosflm (spot picking) finds the > cell 34 34 34 90 90 90 (pointless indicating P41212) > > Structure was solved by SAD phasing on the phosphates > in this space group. Double helices stack in continuous > helices, the backbone is well defined in the (refined) > density maps but the individual bases are messy (purines and > pyrimidines seemed to overlap) + obviously not all spots were > covered and the duplex does not fit in the A.U. > > For this reason the integration was repeated in the > higher cell 34 34 170 > Space group most probably P212121, but solutions can be > found in P41212 as well (still disordered bases) > > There are also indications that the 41 screw axis is > rather a pseudo axis than a pure crystallographic one, also > in the small cell > > Reindexing the cell to 34 34 340 also gives a solution, > which supports the theory of Holton > > Rmerg is around 5% for the small cell, about 8% for the > 170Å cell (both in P41212) > > > > Which refinement procedure would be best to follow? > > kind regards > > Margriet > > > > > > Margriet Ovaere > Chemistry Department K.U.Leuven > Biomolecular Architecture > Celestijnenlaan 200 F > B-3001 Heverlee (Leuven) > Tel: +32(0)16327477 > > > > > > Disclaimer: > http://www.kuleuven.be/cwis/email_disclaimer.htm for more > information. > > > > Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). 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