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 >
