Polymorphs are another possibility. The packing could be very similar but
the space
group could be different.
Enrico.
On Thu, 17 Jan 2013 15:30:20 +0100, Eleanor Dodson
<[log in to unmask]> wrote:
> Hard to say without data - but I would generate the 3 symmetry copies of
> the molecule you would have in P213,
> then do rigid refinement of those coordinates with the P212121 cell
> dimensions and symmetry. There are so many possibilities for origin
> shifts
> But you don't say how non-equivalent the axes are; - if -18.16 ~ 1/4 ~
> 21.39 that is a pretty big difference?
> Eleanor
>
> On 17 Jan 2013, at 14:08, Nicholas Keep wrote:
>
>> I have a structure which normally crystallises in P213 but one data set
>> the edges became slightly non-equivalent in length by a couple of
>> angstroms and the data process in P212121
>>
>> P212121 symmetry operators appears to be a subset of P213
>>
>> http://img.chem.ucl.ac.uk/sgp/large/019az1.htm
>> http://img.chem.ucl.ac.uk/sgp/large/198az1.htm
>>
>> (Not absolutely sure the above are world viewable)
>>
>> Naively I expected the two structures to roughly align. However they
>> don't there appears to be some change of axes between them.
>> The transform of the P213 onto the P212121 structure is
>> 0.03345 -0.9977 -0.0598
>> -0.9994 0.03402 -0.08653
>> 0.01066 0.05929 -0.9982
>> -18.16 -57.18 21.39
>>
>> This is clearly close to
>>
>> 0 -1 0
>> -1 0 0
>> 0 0 -1
>> -0.25 -.75 0.25 in fractionals.
>>
>> Applying either the exact transformation or the regularised one
>> with ether indexing of p213 ie original and k h -l
>> http://www.ccp4.ac.uk/html/reindexing.html
>> the rfactors are well above 50% and don't drop.
>>
>> Any suggestions of what I am doing wrong or is this not going to work
>> (tried MR into the reindexed data and that does not align either- in
>> fact I have tried quite a lot things)
>>
>> The reason for trying to get the two structures on the same axes is to
>> compare the electron densities. The P212121 seems to have some of the
>> disorder loops better defined.
>>
>> Using the Coot transform map by LSQ superpose is quite good BUT it would
>> be better if it were another map other than the refinement map that is
>> transformed as I then want to refine the unmoved structure into the
>> unmoved map guided by the moved map and that involved a lot of changes
>> of map selection.
>>
>> Thanks
>> nick
>>
>>
>>
>> --
>> Prof Nicholas H. Keep
>> Executive Dean of School of Science
>> Professor of Biomolecular Science
>> Crystallography, Institute for Structural and Molecular Biology,
>> Department of Biological Sciences
>> Birkbeck, University of London,
>> Malet Street,
>> Bloomsbury
>> LONDON
>> WC1E 7HX
>>
>> email [log in to unmask]
>> Telephone 020-7631-6852 (Room G54a Office)
>> 020-7631-6800 (Department Office)
>> Fax 020-7631-6803
>> If you want to access me in person you have to come to the
>> crystallography entrance
>> and ring me or the department office from the internal phone by the door
>>
>>
>> --
>> Prof Nicholas H. Keep
>> Executive Dean of School of Science
>> Professor of Biomolecular Science
>> Crystallography, Institute for Structural and Molecular Biology,
>> Department of Biological Sciences
>> Birkbeck, University of London,
>> Malet Street,
>> Bloomsbury
>> LONDON
>> WC1E 7HX
>>
>> email [log in to unmask]
>> Telephone 020-7631-6852 (Room G54a Office)
>> 020-7631-6800 (Department Office)
>> Fax 020-7631-6803
>> If you want to access me in person you have to come to the
>> crystallography entrance
>> and ring me or the department office from the internal phone by the door
--
Enrico A. Stura D.Phil. (Oxon) , Tel: 33 (0)1 69 08 4302 Office
Room 19, Bat.152, Tel: 33 (0)1 69 08 9449 Lab
LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE
http://www-dsv.cea.fr/en/ibitecs/simopro/ltmb/cristallogenese
http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html
e-mail: [log in to unmask] Fax: 33 (0)1 69 08 90 71
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