[phenixbb] Where to find optimized wxc_scale/wxu_scale weighting factors after optimization

Engin Özkan eozkan at stanford.edu
Fri Aug 13 11:44:44 PDT 2010

Thank you Pavel for the great piece of software, and for being very prompt and responsive to users' problems and suggestions.


----- Original Message -----
From: "Pavel Afonine" <pafonine at lbl.gov>
To: phenixbb at phenix-online.org
Sent: Thursday, August 12, 2010 10:03:23 PM
Subject: Re: [phenixbb] Where to find optimized wxc_scale/wxu_scale weighting factors after optimization

  Hi Engin,

> Having the optimized weight printed would be mildly handy. First, the 
> weight is probably not changing wildly between cycle to cycle, so an 
> approximately working wxc_scale can be gotten. Then, this number can 
> be used for quicker test runs with optimize_wxc=false, and you would 
> not worry that your weights are hugely non-optimal for your quick runs.

I agree. The weight for coordinate refinement is reported in log file. 
The weight for ADP refinement is not reported because of a printing bug 
that I will fix.

> Second, I recently realized that in the auto mode for optimize_wxc, my 
> first cycle was not optimizing wxc, and I was getting huge jumps in 
> geometry and R factors in the first cycle. If there was an obvious 
> table showing wxc/wxu per cycle, it would take me shorter to realize 
> what was going on. This first-cycle problem was serious, since it was 
> breaking up all the sensible geometry that I spent days building in a 
> low-resolution, large structure, which wasn't getting fixed in 
> subsequent cycles (Obviously, setting optimize_wxc to every_cycle mode 
> would have prevented this problem, but I bet you that most users 
> aren't aware of such an option. You can also get the optimized 
> wxc_scale by a simple multiplication if you dig into the log file, but 
> that should not be necessary).

Ok, I will add the weight to the table of values that phenix.refine 
outputs by the end of each refinement.

Thanks for always useful feedback!

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