This seems to be very a common scenario in MR and recently we have added 
some code to phaser.MRage that would handle it automatically. Each partial 
solution is analysed for the presence of (complete of incomplete) 
assemblies that obey local point group symmetry. After such an assembly is 
identified, the program can either "fill in" molecules where they should be 
(provided the obey the previously identified local symmetry), and can also 
search with the full assembly. This greatly enhances the signal (since the 
model comprises a larger fraction of the asymmetric unit), and also speeds 
up the search.

(MRage is not yet included in the current CCP4 release, but available as 
alpha-test in recent Phenix nightly builds.)

BW, Gabor

On Apr 30 2012, Roger Rowlett wrote:

>A partial solution can potentially lead you to an appropriate MR 
>solution. With many protein chains in the ASU,  there will be several 
>"reasonable" possibilities by Matthews analysis. When I originally 
>solved 2A8D, cell content analysis suggested 8 monomers per ASU, but it 
>was clear after a few MR runs that was not going to work. Inspecting the 
>packing of a partial solution with 4 monomers, which formed a nice, 
>biological-looking tetramer, clearly suggested that another dimer would 
>fit into the lattice just nicely. A search with 3 such dimers produced 
>an excellent MR solution starting point for the final refinement. I used 
>a similar procedure for 3UAO. The Matthews analysis suggested 10-12 
>chains per ASU, but it was clearly 8 based on packing of partial 
>solutions. A 4-dimer search was immediately successful.
>
>Cheers,
>
>_______________________________________
>Roger S. Rowlett
>Gordon & Dorothy Kline Professor
>Department of Chemistry
>Colgate University
>13 Oak Drive
>Hamilton, NY 13346
>
>tel: (315)-228-7245
>ofc: (315)-228-7395
>fax: (315)-228-7935
>email: [log in to unmask]
>
>On 4/30/2012 5:20 PM, [log in to unmask] wrote:
>> Provided that you guess the number of copies and your guess is 
>> reasonably close, my experience is that Phaser will do the job. But 
>> you have to tell it how many copies you expect, or it will never make 
>> sense of the data. When I did my structure with 6(?) copies some years 
>> ago, I guessed a number that was close enough and then when I 
>> inspected the electron density I could see that there were more copies 
>> than I had told the software and all was fine after that. It was 
>> surprising to see that good solutions were obvious from a packing 
>> consideration, while inadequate solutions were obviously wrong.
>>
>> Mark
>>
>>
>> -----Original Message-----
>> From: Ke, Jiyuan <[log in to unmask]>
>> To: CCP4BB <[log in to unmask]>
>> Sent: Mon, Apr 30, 2012 2:28 pm
>> Subject: [ccp4bb] Suggestions for solving a structure with 8-10 copies 
>> per asymmetric unit
>>
>> Dear All, I have a question regarding solving a crystal structure by 
>> molecular replacement. It is a single protein with a molecular weight of 
>> 25.5 kDa. The cell dimension is rather big from the diffraction data ( 
>> 90.9 Å, 143.9 Å, 216.3Å, 90°, 90°, 90°). The possible space group is 
>> P212121. With such a big unit cell, we predicted that there are 8-10 
>> molecules per asymmetric unit. We have a decent model with sequence 
>> similarity of 49%. I tried several times with Phaser search with the 
>> current model and had difficulty to find any clear solution. Has anyone 
>> seen such cases and any suggestions to solve the structure? Thanks! 
>> Jiyuan Ke, Ph.D. Research Scientist Van Andel Research Institute 333 
>> Bostwick Ave NE Grand Rapids, MI 49503
>

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     Dr Gabor Bunkoczi

     Cambridge Institute for Medical Research
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