Another factor may be that phenix.refine does not make a full use of
experimental phase information in its calculation of the error
parameters - I've been discussing this with Peter, Randy and Ralph. I
don't know that this is the cause, but I see inferior results when
recycling buccaneer with phenix.refine (although this is confounded by
the fact that phenix.refine doesn't output the updated ABCD's. Having
said that, neither does refmac, but it does give me something I can
fudge. Both Garib and Pavel could toss me a bone here).
A corollary is that phenix.refine may also not use the experimental
phase information in its map coefficients - I simply assumed that it
did, but that assumption may be unwarranted.
Both of these factors would affect the quality of the maps when refining
with experimental phasing (assuming a good modern phasing program).
However if the difference is also present after MR, then you need to
look elsewhere for an explanation.
Kevin
Dunten, Pete W. wrote:
>
>
> I mentioned previously phenix.refine tosses your weak data if IMEAN,
> SIGIMEAN are chosen during refinement.
>
>
>
> I’m wondering if this omission of weak Fobs from the Fobs-Fcalc
> difference map explains why the difference maps out of refmac seem to be
> more helpful in showing where to move atoms.
>
>
>
> D. Crowfoot et al. in The Chemistry of Penicillin (1949) explain why
> this might be so, and Stout & Jenson elaborate the argument. Briefly,
> the calculated phase will be closest to the phase of the vector
> difference Fcalc – Fobs when |Fcalc| > |Fobs|.
>
>
>
> I leave it to the reader to try calculating some maps with and without
> the weak Fobs in phenix.refine or refmac, and perhaps making some
> deliberate rotamer errors, to see if using the complete data with weak
> Fobs helps.
>
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