Can one make it? If so, what's the keyword? Because I couldn't it in
the online docs.
Cheers
phx
Peter Zwart wrote:
> phenix.refine also might not (by default) use missing data in map calculation.
> AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe
> this changed now).
> When your high resolution shells are incomplete (like when using the
> anisotropy server to perform elliptical data truncation, or etc etc),
> I can imagine that the use of DFc can have considerable effect on the
> looks of a map.
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> P
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> 2008/9/28 Kevin Cowtan <[log in to unmask]>:
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>> 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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