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NO do NOT invert the hand. If you do you will end up with left-handed helices etc The alternative indexing systems all need to preserve the right-handed axis system imposed by the data integration program (eg k,h,-l) The ONLY time it is valid to invert the hand is if the indexing/integration program itself inverted the hand due to a bug (this has been know, but not for a long time) Phil On 29 May 2012, at 12:55, Mark J van Raaij wrote: > In different datasets of P321 crystals, when you index them separately, the hand may be different and you may need to invert it for some. They "prohibition" in reindex is really a warning, and can be overridden. > > Mark J van Raaij > Laboratorio M-4 > Dpto de Estructura de Macromoleculas > Centro Nacional de Biotecnologia - CSIC > c/Darwin 3 > E-28049 Madrid, Spain > tel. (+34) 91 585 4616 > http://www.cnb.csic.es/~mjvanraaij > > > > On 29 May 2012, at 13:52, Ian Tickle wrote: > >> In principle there's no reason why you can't invert the hand of the >> indices, as long as the program which does it also takes care to >> convert any hand-dependent columns such as anomalous differences, >> F+/F- etc in the appropriate manner at the same time. The program >> will also need to convert any phase or phase-coefficient columns, but >> it will have to do this anyway, even if the hand is not inverted, in >> those cases where the space group contains screw axes (since then you >> will get phase shifts on reindexing for certain subsets of >> reflections). >> >> So if the data consist only of I's or F's without anomalous data or >> phases then inverting the hand will have absolutely no effect (it's >> called "Friedel's Law"). >> >> I note from the documentation that reindex will invert the hand if the >> keyword 'LEFT' is supplied, though whether it then treats the >> anomalous data and phases correctly is anyone's guess! >> >> The question is really whether it's likely ever to be _necessary_ to >> invert the hand; this will depend on the reciprocal space asymmetric >> unit chosen by the processing program. One could imagine a situation >> where the a.u. chosen by one processing program was on a different >> hand from the a.u. required by another. In such a situation you would >> have no choice but to invert the hand of the indices, though I suspect >> you would be better off doing it with CAD which will do it reliably, >> rather than reindex which may not (judging by the comments in the >> reindex code!). Whether such a situation ever occurs in practice, I >> don't know, maybe not. >> >> Cheers >> >> -- Ian >> >> On 29 May 2012 09:57, Graeme Winter <[log in to unmask]> wrote: >>> Hello Qixu Cai, >>> >>> What you want is a reindexing operator which permutes the axes rather >>> than one which changes the sign of an axis. The easiest way to do this >>> is with pointless: >>> >>> pointless hklin input.mtz hklref reference.mtz hklout output.mtz >>> >>> and let pointless figure out the right operation to use. You may find >>> the following helpful: >>> >>> http://www.ccp4.ac.uk/html/reindexing.html >>> >>> Best wishes, >>> >>> Graeme >>> >>> On 29 May 2012 09:48, Qixu Cai <[log in to unmask]> wrote: >>>> Dear all, >>>> >>>> I have a dataset at P321 space group. And I want to reindex from (h,k,l) to >>>> (k,h,l) or (h,k,-l), because I want to merge this dataset to the native >>>> dataset. >>>> At first, I used the "reindex" program in CCP4i, and got an error: (either >>>> for (k,h,l) or (h,k,-l)) >>>> >>>> ================================================ >>>> Data line--- reindex HKL h, k, -l >>>> Data line--- end >>>> >>>> $TEXT:Warning: $$ comment $$ >>>> WARNING: !!!! Reindexing matrix INVERTS hand !!!! >>>> $$ >>>> REINDEX: !!!! You are NOT allowed to do this - Changing all signs in >>>> reindexing matrix >>>> Times: User: 0.0s System: 0.0s Elapsed: 0:00 >>>> ================================================= >>>> >>>> Could you please tell me the reason? >>>> >>>> At last, I converted the mtz file to CNS format, and write a script to >>>> exchange the h and k, and converted to mtz file. >>>> When I tried to use "cad" to merge this dataset to the native dataset, if I >>>> chose "Automatically check and enforce consistent indexing between different >>>> files", >>>> the index would be changed back to the original index. Why? >>>> >>>> Thank you very much for your attention. >>>> >>>> Best wishes, >>>> >>>> Qixu Cai