Re: [ccp4bb]: R32 pseudotranslational symmetry in crystal

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Christopher Lehmann wrote:
> Dear Manoj,
> 
> How sure are you that the orientation of the second molecule is correct?


  If the native Patterson has a large off origin peak, then you must 
have two molecules in the same orientation. So if the patterson peak is 
at Xp, Yp, Zp and you have a molecule fixed somewhere there must be another
with coordinates either x+Xp, y+Yp z+Zp, or x-Xp, y-Yp z-Zp.

Just what constitutes "large off origin peak" is a bit problematic. We 
usually say > 20% of origin of 4A native Patterson, but it depends.
It is a good idea once you have fixed your 2 molecules to run a cycle of 
rigid body refinement with FITFUN if you are using Amore or REFMAC5 to 
refine the relative orientations. This is less effective if the 
translation is very close to 0,0,1/2 though.
eleanor
> If I understand your add correctly, you had one solution in the
> rotation search and two in translation search. Does the patterson
> confirm this finding? You could try EPMR, just for the fun.
> 
> However these Space groups can be tricky and/or twinned.
> 
> Yours
> (:hristopher
>  
> 
> "N.Manoj" wrote:
> 
>> ***  For details on how to be removed from this list visit the  ***
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>>
>> Dear all,
>>           We have a problem in refining a structure in space group R32.
>> The data processed to 2.9A with  overall Rmerge of 5%, 98% completeness
>> and redundancy of 5. AMoRe gave clear solutions for the two expected
>> molecules in the asymmetric unit. The packing looked good,  but the
>> structure could not be refined below 45% R-factor. Electron density for
>> one monomer is good while it is very poor for the other monomer.
>> The two molecules are identical (same rotation function values) in
>> orientation and are translated by almost 1/2 along the Z axis. I would
>> like to know if there is some way of going about refining this
>> structure.
>> I remember some discussion about refinement of structures with  pseudo
>> translational symmetry in the ccp4 BB some time back.
>>
>> Thanks in advance
>> manoj
>>
> -- 
> Dr. Christopher Lehmann
>  
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