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