[ccp4bb]: A question about MR:self rotation

["Rainbow Yun" <superyunch@moon.ibp.ac.cn>]

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Hi! Everybody,

I am a beginner in Protein Crystallography. Recently I am trying Molecular Replacement to solve the  structure of an unkown protein. I have got several models from PDB£¬ and the sequence of my protein shows high homology to the models as >80. And I know that in the crystal of my protein (P212121), one asymmetrical unit contains only one protein molecule. It seems that this should be a very easy work, but this turns out to be not true. According to the models, the protein should contain two global domains connected by an alhpa-helix which is a bit flexible, and the two domains are very similar to each other (three dimensional structure, not sequence: main chain and side chain). I have tried to use either domain to search for solution but found that both result in a same solution. This means that one one domain of my protein was found and the "other" domain cannot be found. So I tried to check the unoutstanding solutions given by the MR program. To do that I want to firstly fi!
 nd the rotation matrix between the two domains (supposing they are also similar to each other like the models). It seems that Self Rotation function can do this work, but unfortunately I tried several program and could not find a solution which can explain some two solutions given by the cross-rotation functuion. So I want to know if this idea is wrong or unpractical. And if not, how can I solve this problem.  

Thank you.
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Rainbow Yun
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡superyunch@moon.ibp.ac.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2002-08-28