Thanks for your help. How to override the warning?
2012/5/29 Mark J van Raaij <mjvanra...@cnb.csic.es> > 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 >
