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.
P
2008/9/28 Kevin Cowtan <[EMAIL PROTECTED]>:
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.
