[phenixbb] PHASER-TFZ scores with ensembles higher?

[Gabor Bunkoczi]

Dear Jan,

MRage is running Phaser code behind the surface, so the two should perform 
equally. However, the output format is different, and right now this 
prevents you from running the ensemble reduction procedure. As a 
workaround, you could re-run the molecular replacement with MRage, just to 
try it out. On the longer run, we will make it work with Phaser output, if 
it proves useful.

BW, Gabor

On Jun 28 2013, Jan Gebauer wrote:

>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
>>>
>>
>
>
>