[phenixbb] R, Rfree, and wxu_scale
Jianghai Zhu
jzhu at cbr.med.harvard.edu
Sat Aug 4 19:43:51 PDT 2007
Yes, yes. But before one admits the model with the higher Rfree is
the more accurate model, one must make sure the refinement protocol
is correct.
Jianghai
+++++++++++++++++++++++++++++++
Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232
+++++++++++++++++++++++++++++++
On Aug 4, 2007, at 10:06 PM, Mayer, Mark (NIH/NICHD) [E] wrote:
> Forgive me for saying this but the object of refinement is to build
> the most accurate model, not to obtain the lowest Rvalue,
> which will vary with weights applied to diffraction data versus
> constraints. There have been multiple posts about this on
> crystallographic BBs in the last few months ...
>
>
> -----Original Message-----
> From: Jianghai Zhu [mailto:jzhu at cbr.med.harvard.edu]
> Sent: Sat 8/4/2007 9:19 PM
> To: PHENIX user mailing list
> Subject: [phenixbb] R, Rfree, and wxu_scale
>
> Hi,
>
> Just finished a round of refinement. Rfree went up about 1% and R
> went down a bit. I am wondering what happened here. Also Rfree
> always went down after TLS refinement but always went up a lot more
> after the individual ADP refinement. Is there anything I can do
> here? Should I use weaker B restraints? I tried to assign a
> wxu_scale value. But phenix.refine automatically adjust it to 1.81
> every time.
>
> ----------------------------------------------------------------------
> --
> R-factors, x-ray target values and norm of gradient of x-ray target
> stage r-work r-free xray_target_w xray_target_t
> 0 : 0.3982 0.5701 6.156859e+00 6.238509e+00
> 1_bss: 0.2008 0.2494 5.949117e+00 6.088855e+00
> 1_xyz: 0.2030 0.2497 5.953829e+00 6.091696e+00
> 1_adp: 0.1998 0.2559 5.952833e+00 6.099340e+00
> 2_bss: 0.1996 0.2557 5.952517e+00 6.099196e+00
> 2_xyz: 0.1984 0.2576 5.953246e+00 6.104085e+00
> 2_adp: 0.1974 0.2578 5.950434e+00 6.102336e+00
> 3_bss: 0.1972 0.2574 5.950333e+00 6.102222e+00
> 3_xyz: 0.1997 0.2576 5.956524e+00 6.103647e+00
> 3_adp: 0.1987 0.2590 5.955554e+00 6.104434e+00
> 3_bss: 0.1986 0.2588 5.955445e+00 6.104227e+00
> ----------------------------------------------------------------------
> --
> Weights for target T = Exray * wxc * wxc_scale + Echem * wc and
> angles between gradient vectors, eg. (d_Exray/d_sites, d_Echem/
> d_sites)
> stage wxc wxu wxc_sc wxu_sc /_gxc,gc /_gxu,gu
> 0 : 5.5611e-01 7.2249e-01 0.050 1.810 96.334
> 101.736
> 1_bss: 5.5611e-01 7.2249e-01 0.050 1.810 96.334
> 101.736
> 1_xyz: 4.5001e-01 6.1023e-01 0.050 1.810 96.591
> 102.016
> 1_adp: 4.5001e-01 6.1023e-01 0.050 1.810 96.591
> 102.016
> 2_bss: 4.5001e-01 6.1023e-01 0.050 1.810 96.591
> 102.016
> 2_xyz: 5.1326e-01 6.5356e-01 0.050 1.810 112.802
> 141.393
> 2_adp: 5.1326e-01 6.5356e-01 0.050 1.810 112.802
> 141.393
> 3_bss: 5.1326e-01 6.5356e-01 0.050 1.810 112.802
> 141.393
> 3_xyz: 3.3568e-01 7.0695e-01 0.050 1.810 111.975
> 135.760
> 3_adp: 3.3568e-01 7.0695e-01 0.050 1.810 111.975
> 135.760
> 3_bss: 3.3568e-01 7.0695e-01 0.050 1.810 111.975
> 135.760
> ----------------------------------------------------------------------
> --
>
> Jianghai
>
> +++++++++++++++++++++++++++++++
> Jianghai Zhu, Ph.D
> CBR Institute for Biomedical Research
> Department of Pathology
> Harvard Medical School
> 200 Longwood Ave., Boston, MA 02115
> Ph: 617-278-3211
> Fx: 618-278-3232
> +++++++++++++++++++++++++++++++
>
>
>
>
> <winmail.dat>
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