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 <graeme.win...@gmail.com> 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 <caiq...@gmail.com> 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
