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CCP4BB  December 2018

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Subject:

Re: Experimental phasing vs molecular replacement

From:

James Holton <[log in to unmask]>

Reply-To:

James Holton <[log in to unmask]>

Date:

Thu, 6 Dec 2018 11:01:32 -0800

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Sorry for the confusion, I was going for brevity.

Any time you do a thought experiment you make a fake-data data set, the 
"true" phases and "true" amplitudes become the ones you put into the 
simulation process.  This is by definition.  Is there potential for 
circular reasoning?  Of course!  But you can do controls:

   If you start with an ordinary single-conformer coordinate model and 
flat bulk solvent from refmac to make your Ftrue, then what you will 
find is that even after adding all plausible experimental errors to the 
data the final Rwork/Rfree invariably drop to small-molecule levels of 
3-4%.  This is true even if you prune the structure back, shake it, and 
rebuild it in various ways.  The difference features always guide you 
back to Rwork/Rfree = 3/4%. However, if you refine with phenix.refine, 
you will find Rwork/Rfree stall at around 10-11%.  This is because Ftrue 
came from refmac and refmac and phenix.refine have somewhat different 
bulk solvent models.  If Ftrue comes from phenix and you refine with 
refmac you get similar "high" R values.  High for a small molecule 
anyway. And, of course, if you get Ftrue from phenix and refine with 
phenix you also get final Rwork/Rfree = 3/4%. If you do more things that 
automated building doesn't do, like multi-headed side chains, or get the 
bulk solvent from an MD simulation, then you can get "realistic" 
Rwork/Rfree in the 20%s.  All of this is the main conclusion from this 
paper: https://dx.doi.org/10.1111/febs.12922

But, in all these situations with various types of "systematic error" 
thrown in, because you know Ftrue and PHItrue you can compare different 
kinds of maps to this ground "truth" and see which is closest when you 
compare electron density. In my experience, this is the 2mFo-DFc map, 
phased with PHIcalc from the model. You might think that replacing 
PHIcalc with PHItrue would make the map even better because PHItrue is a 
"better" phase than PHIcalc, but it turns out this actually make things 
worse!  That's what is counter-intuitive: 2mFo-DFc amplitudes are 
"designed" to be used with the slightly-wrong phase of PHIcalc, not 
PHItrue.

That's what I was trying to say.

-James Holton
MAD Scientist


On 12/5/2018 7:36 PM, Keller, Jacob wrote:
>>> That said, model phases are not so bad.  In fact, in all my experiments with fake data the model-phased 2mFo-DFc map always has the best correlation to the "true" map.  If you substitute the "true" phases and use the 2mFo-DFc coefficients you actually make things worse. Counter-intuitive, but true.
> I don't understand what you mean by true and fake here--can you clarify? How are the true map and phases generated (from an original true model, I assume?), and how are the fake data generated? (Also from the true model?) I am wondering whether there is some circular reasoning?
>
> JPK

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