[phenixbb] Weight optimization
PAfonine at lbl.gov
Tue May 25 15:45:03 PDT 2010
try adjusting these values to match your expectations:
bonds_rmsd_max = 0.05
angles_rmsd_max = 3.5
I've never really played with this, but this is done exactly to address
your question. That weight will be selected that minimizes the Rfree and
obeys the above limits. I'm not sure what happens if you already start
with the values that are higher than these limits.
Please let me know if you have any problems with this.
On 5/25/10 9:08 AM, Jianghai Zhu wrote:
> I am using the optimize_wxc=true and optimize_wxu=true in my last refinement. The R and Rfree went down but the RMSDs were way too large. I wonder if phenix.refine still targets the geometry when it optimizes the R and Rfree. Here are the results from almost two identical runs except the weight optimization.
> 1) optimize_wxc = False optimize_wxu = False wxc_scale=0.08 wxu_scale=1.66
> results: R=0.2294 R-free=0.2709 angl=1.087 bond=0.006
> 2) optimize_wxc = True optimize_wxu = True wxc_scale=0.08 wxu_scale=1.66
> results: R=0.2141 R-free=0.2628 angl=2.894 bond=0.033
> I am using the dev-412 version. Thanks.
> -- Jianghai
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