Qixu, yes obviously any sub-group is a possible indexing (all the way down to P1 !). You need to compare your Rpims etc.
Cheers -- Ian On 29 May 2012 15:03, Qixu Cai <caiq...@gmail.com> wrote: > P3 is another possible alternate indexing? is that correct? > > > > 2012/5/29 Ian Tickle <ianj...@gmail.com> >> >> Mark, thanks for pointing that out, I see it now: >> >> In P321 the only possible alternate indexing is (-h, -k, l): this is a >> 2-fold || c which is an operator of the hexagonal lattice but is not >> an equivalent reflection. >> >> The standard CCP4 a.u. is h = k, l >= 0 or h > k, k >= 0, so for >> example (3,2,1) would be in the standard a.u. (3 > 2 and 2 >= 0). In >> the alternate indexing this would be (-3, -2, 1); however it's >> impossible to transform this to the a.u. with any non-inverting >> equivalent. The only possibility is to invert the hand, i.e. to (3, >> 2, -1) which is again in the a.u.. >> >> So the required re-indexing operator to match (3, 2, -1) with (3, 2, >> 1) is (h, k, -l) which reindex won't allow without the LEFT keyword >> (and you would be well-advised to avoid doing it with phase columns!). >> >> Cheers >> >> -- Ian >> >> On 29 May 2012 12:55, Mark J van Raaij <mjvanra...@cnb.csic.es> 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 <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 > >
