Re: [ccp4bb]: A question about MR:self rotation

["David J. Schuller" <djs63@cornell.edu>]

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On Wed, 28 Aug 2002, Rainbow Yun wrote:

> 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.  

if you are finding one domain with your MR procedure, refine and 'FIX' 
that solution, then search for a second one.  this should be possible with 
most MR packages.
if the first domain solution is accurate, that should place packing and 
orientation restraints on the second domain, which could be used to 
evaluate possible solutions.

if MR fails, there are always SIR, MIR, MAD, etc.  short halogen soaks are 
probably the easiest to try, unless your protein happens to have an 
anomalous scatterer incorporated in the structure.

cheers,
=======================================================================
Life is a struggle, not against sin, not against the Money Power, not 
against the malicious animal magnetism, but against hydrogen ions.
                                                - H.L. Mencken
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                        David J. Schuller
                        modern man in a post-modern world
                        MacCHESS, Cornell University
                        djs63@cornell.edu