[phenixbb] ? about optimize weights
Pavel Afonine
PAfonine at lbl.gov
Wed Oct 15 09:56:30 PDT 2008
Hi Gerwald,
> I just started using phenix.refine and it's working quite well so far. I
> ran the optimize weight strategy at the end of a test refinement and it
> lowered the Rfree as intended. Unfortunately, when I ran the next refine
> job based on the output .def file, it seems that the 'best weights'
> found in the previous run were not conserved as the geometry and R
> factors got a lot worse.
>
The "best weights" are good per macro-cycle. That is what is the "best
weight" for macro-cycle #1 is not necessarily the best one for
macro-cycle #2, etc. This is why they are not preserved for next runs.
> Where can I find the weights determined by the optimize run and how can
> I fix those for further refinement?
>
If you run phenix.refine with "optimize_wxc=true", then you will see
something like this:
================================ xyz refinement
===============================
Start r_work= 0.2359 r_free= 0.2576 bonds= 0.004 angles= 1.08
r_work= 0.2304 r_free= 0.2504 bonds= 0.003 angles= 1.14 scale= 1.00
r_work= 0.2286 r_free= 0.2476 bonds= 0.003 angles= 1.22 scale= 1.40
r_work= 0.2279 r_free= 0.2465 bonds= 0.004 angles= 1.26 scale= 1.80
r_work= 0.2271 r_free= 0.2454 bonds= 0.004 angles= 1.32 scale= 2.20
r_work= 0.2266 r_free= 0.2447 bonds= 0.005 angles= 1.35 scale= 2.60
r_work= 0.2262 r_free= 0.2442 bonds= 0.005 angles= 1.39 scale= 3.00
r_work= 0.2258 r_free= 0.2436 bonds= 0.005 angles= 1.41 scale= 3.40
r_work= 0.2256 r_free= 0.2433 bonds= 0.006 angles= 1.44 scale= 3.80
r_work= 0.2253 r_free= 0.2429 bonds= 0.006 angles= 1.47 scale= 4.20
r_work= 0.2251 r_free= 0.2426 bonds= 0.006 angles= 1.49 scale= 4.60
r_work= 0.2249 r_free= 0.2425 bonds= 0.007 angles= 1.51 scale= 5.00
r_work= 0.2245 r_free= 0.2417 bonds= 0.008 angles= 1.56 scale= 6.00
r_work= 0.2242 r_free= 0.2420 bonds= 0.008 angles= 1.60 scale= 7.00
r_work= 0.2238 r_free= 0.2408 bonds= 0.009 angles= 1.63 scale= 8.00
r_work= 0.2236 r_free= 0.2413 bonds= 0.010 angles= 1.68 scale= 9.00
r_work= 0.2234 r_free= 0.2409 bonds= 0.010 angles= 1.71 scale= 10.00
r_work= 0.2314 r_free= 0.2516 bonds= 0.003 angles= 1.11 scale= 0.85
r_work= 0.2331 r_free= 0.2538 bonds= 0.003 angles= 1.05 scale= 0.70
r_work= 0.2362 r_free= 0.2566 bonds= 0.003 angles= 0.98 scale= 0.55
Final r_work= 0.2238 r_free= 0.2408 bonds= 0.009 angles= 1.63
In this particular case, the best result is:
r_work= 0.2238 r_free= 0.2408 bonds= 0.009 angles= 1.63 scale= 8.00
meaning that if you want to fix it then "wxc_scale=8" keyword in your
subsequent phenix.refine run (I should replace "scale" with "wxc_scale"
to make it more obvious).
Pavel.
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