P3 is another possible alternate indexing? is that correct?


2012/5/29 Ian Tickle <[log in to unmask]>
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 <[log in to unmask]> 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