phenix.refine updates weight every macro-cycle. It is true that a good weight for macro-cycle 1 does not have to be a good weight for macro-cycle 2, and a good weight for mc 2 is not necessarily good for mc 3, etc. This is one of reasons why doing just one macro-cycle isn't best idea in general, unless you are experimenting with something particular. Weight calculation used in phenix.refine isn't something I invented. We use protocol implemented by Axel Brunger back in 1989 in X-plor and since then nobody came up with a better way to do this (I did spend quite some time investigating this matter). Alternative way to calculate weight is implemented in TNT (by Dale Tronrud); likely Refmac uses same idea. This is dictated by the minimizer they use, which is 2nd derivatives-based. Pavel On 5/4/17 14:26, Phil Jeffrey wrote:
But the variable weighting scheme that phenix.refine uses actually causes problems with this - the optimal weight(s) for cycle 1 is most assuredly not the optimal weight for cycles 2....n and it even does this with converged high resolution structures, so it's not just a result of the usual violence I do to structures when rebuilding them.
I think this trend of the first cycle weight being an outlier is quite possibly the source of what Pat is seeing, and it's not clear to me why phenix.refine does this where I see a lot less of it (if any at all) in Refmac.
Phil Jeffrey Princeton
On 5/4/17 2:36 PM, Schnicker, Nicholas J wrote:
Hi Pat,
I believe they suggest using target weight optimization in this case. It can be specified on the command line as below:
optimize_xyz_weight=true optimize_adp_weight=true
I've found for a couple structures I had to use this or else the geometry was much worse. They also recommend to use this in the last round of refinement.
Cheers,
Nick
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