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 [email protected] > 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 [email protected] > 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
