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Re: [ccp4bb] P21, twinned date & NCS refinement |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: P21, twinned date & NCS refinement From: "Bosch, Juergen" jubosch {- at -} JHSPH {- dot -} EDU Date: 2012-03-27 Thanks Garib for your input. And yes we do see some split spots. We used XDS to overcome (I hope) most problems but still intensities of perfectly overlapping reflections will be too large. Would you think it's safer to integrate the data in P1 as symmetry mates will not be merged and then solve in P1 and convert into P21 cell for further refinement afterwards ? Jürgen On Mar 27, 2012, at 4:53 PM, Garib N Murshudov wrote: I would say that you should use ncs restraints in any case. NCS relates atoms and twin relates intensities. In some sense presence of twinning reduces information contents (in the limiting case the number of (effective) observervations becomes twice less) of the data and using NCS decreases the effective number of adjustable parameters. Without NCS some of the stats (like RvR) cannot be trusted. However you should remember that if ncs is very close to twin operators then in reciprocal space they relate two reflections exactly and in most of the cases you do not gain much and differences between ncs related molecules might be more important than their similarity. I would suggest using local ncs then global differences are retained and molecules are made locally similar. If bet angle is 92.4 degrees (I would also check obliquity in refmac output if you are using that. In your case this number should be non-zero, meaning that twin related reflections will not coincide exactly) then I would expect splitting of spots in some directions at high resolutions. One should be careful when integrating, if only one of these spots are integrated then you may end up have several classes of reflections: low resolution and in some directions when spots overlap perfectly you have contributions from two crystals, in split spot cases each spot has contribution from single crystal. regards Garib On 27 Mar 2012, at 21:37, Bosch, Juergen wrote: Dear CCP4BBers and PhenixBBers (cross posting here, since we all read both anyhow) to the experts out there here's my question: We have a P21 dataset with 2 molecules in the asu and a refined twin fraction of 38% according to phenix.refine using a twin law operator. My gut feeling tells me that I can't use NCS unless I detwin the data, is that a correct assumption ? How does phenix.refine [PDB] [mtz] twin_law="h,-k,-l" main_ncs=true would deal with this problem ? Same question goes to Garib, it's very convenient to just specify twin in your Refmac script without further values and magic happens but what if I add NCS restrains, will Refmac treat them correctly according to the twin operator ? Twins are confusing in real life and even more in crystals I think. And no the data can not be processed in a higher space group, P222 results in Rmerges of >40% in the lowest resolution shell, the beta angle is 92.4 degrees in P21. And if processed in P1 we get 4 molecules per asu and a refined twin fraction of 50%, which in my eyes clearly indicates it's not P1 but really P21. Hope to get some interesting feedback on this issue. Thanks, Jürgen ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/ Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: garib@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/ CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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