NO do NOT invert the hand. If you do you will end up with left-handed helices etc
The alternative indexing systems all need to preserve the right-handed axis system imposed by the data integration program (eg k,h,-l)
The ONLY time it is valid to invert the hand is if the indexing/integration program itself inverted the hand due to a bug (this has been know, but not for a long time)
Phil
On 29 May 2012, at 12:55, Mark J van Raaij 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 <[log in to unmask]> 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 <[log in to unmask]> 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
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