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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