[phenixbb] PHASER-TFZ scores with ensembles higher?
jan.gebauer at uni-koeln.de
Fri Jun 28 08:27:41 PDT 2013
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?
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
>> 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...
Dr. Jan Gebauer
AG Prof. Baumann
Institut für Biochemie / Uni-Köln
Otto-Fischer-Str. 12-14 / 50674 Köln
Fon: +49 (221) 470 3212
Fax: +49 (221) 470 5066
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