[phenixbb] PHASER-TFZ scores with ensembles higher?

[Jan Gebauer]

Dear Gabor,

that sound indeed very interesting...
I haven't used MRage yet. Do you think that is more capable (at least in  
some aspects) than PHASER?

Best,
Jan

Am 28.06.2013, 10:24 Uhr, schrieb Gabor Bunkoczi <gb360 at cam.ac.uk>:

> Dear Jan,
>
> I leave the it for the more knowledgeable to answer your question about  
> the effect of ensembles on TFZ. It is, however, not uncommon that a  
> solution with an ensemble is difficult to refine (at least with a single  
> model), esp. when none of the ensemble members are good models (which  
> you have verified). In this case, you may get better results by building  
> a "chimera" model (recombining parts of the ensembles that match the  
> electron density best) and use that one for refinement. We have  
> implemented an automatic procedure for phaser.MRage output using Tom  
> Terwilliger's phenix.combine_models program, and this could be modified  
> to work with Phaser output as well. Let me know if this were potentially  
> useful for you now.
>
> BW, Gabor
>
> On Jun 28 2013, Jan Gebauer wrote:
>
>> Dear Phaser users,
>>
>> I recently tried to solve two difficult MR jobs by using ensembles in   
>> PHASER.
>> With ENSEMBLES in this case I mean aligned structures prepared for  
>> PHASER  by Phenix.ENSEMBLER.
>> In both case I got solution with rather high TFZ-score (> 8), which I   
>> couldn't get wit individual structure, but was not able to refine them.
>>
>> My question is, whether using ensembles would increase the Z-Score  
>> without really improving phases. In other words, if there is another  
>> cut-off for the "Phaser solved it" Z-score, when using ensemble in  
>> contrast to single structures...
>>
>> Regards,
>> Jan
>>
>


-- 
Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
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