[phenixbb] Different stats with different number of macrocycles

Pavel Afonine pafonine at lbl.gov
Fri May 5 00:03:14 PDT 2017

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.


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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