Thanks for your help. How to use CAD to invert the hand?
2012/5/29 Ian Tickle <ianj...@gmail.com> > 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 >
