Hmm - once you have transformed your co-ordinates by that matrix which is non-crystallographic they are no longer aligned in your unit cell, so you can't apply your symmetry operators to them . I don't think what you are doing is valid, but to be sure I would need to know more about the 2 structures Eleanor On 28 Oct 2012, at 14:07, Appu kumar wrote:
> The space group and unit cells in two pdb are different. In model.pdb it is, > 64.386 69.508 116.859 90.00 90.00 90.00 P 21 21 21 > > > and in our str it is 46.921 105.301 47.751 90.00 103.26 90.00 P 1 21 1 > > on aligning both the structure in coot, the resulting transformation matrix > is attached with this mail. As both Arka Chakraborty and Eleanor Dodson > suggested me to do PISA, I did but i am not getting the correct tetramer > arrangement which i am getting on aligning the our strcture on model > structure first and then genrating the symmetry mates of our structure and > then finally filtering the right tetramer. My question is, generating the > tetramer after aligning the structure, is a right way to find the tetramer. > PDB PISA is not suggesting me the right assembly for tetramer. I making the > tetramer in different way which is not straightforward. I am first allowing > my structure to rotate and translate on model structure and the generating > the symmetry mates for finding the tetramer. I have got the right tetramer > too but i am not sure the way i did is right or wrong. > > > > On 28 October 2012 16:41, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > I think we need more information. > Are the cells and space groups similar > What are the transformations which fit your coordinates to the model > structure? > > Have you submitted your coordinates to the PISA server at the EBI - that will > suggest possible tetramers? > > Eleanor > > > On 28 Oct 2012, at 07:31, Appu kumar wrote: > > > Dear all, > > Please guide me on right track in weired confusion. I > > have model structure(available in pdb) and a structure solved by molecular > > replacement as a dimer . Our structure does not giving correct tetramer by > > symmetry mates. Strangely when i am aligning our structure on model > > structure and generating symmetry mates of our structure to find the > > correct tetramer from dimer, i am getting the one which i want. Why the > > structure solved by us give tetramer on aligning with model structure. I do > > not know weather it is a right way to find the correct oligomeric state of > > protein or not. So please i reaquest you to suggest me with your valuable > > advice to overcome with this confusion. > > Thank you in advance > > Appu > > > <transformation matrix.pptx>
