[phenixbb] Phenix.refine coordinate error estimate discrepancies

[Pavel Afonine]

Hi Phil,

this was a bug in old version of PHENIX that I fixed some time ago. 
Please install the latest version, the one from the nightly builds, 
1.4-115 for example:

http://www.phenix-online.org/download/nightly_builds.cgi

Please let me know if this fixes the problem.

Pavel.



On 7/21/09 12:44 PM, Phil Jeffrey wrote:
> There seems to be a large discrepancy between the likelihood-based 
> coordinate error estimate depending on whether the intensities or 
> structure factor magnitudes are used, which doesn't make any sense to me.
>
> If I do:
>
> % phenix.refine rebuild.pdb data_withI.mtz
>
> phenix.refine picks up Imean and SigImean from the MTZ and refines the 
> structure
>
>      xray_data {
>        file_name = "data_withI.mtz"
>        labels = "IMEAN,SIGIMEAN"
>        r_free_flags {
>          file_name = "data_withI.mtz"
>          label = "FreeR_flag"
>          test_flag_value = 0
>        }
>
> then I get:
>
> | maximum likelihood estimate for coordinate error:   1.39 A 
>
>
>
> But if I create an MTZ file without the intensities by using CAD on the 
> original file, and use the same coordinate file:
>
> % phenix.refine rebuild.pdb data_withoutI.mtz
>
> phenix.refine picks up the structure factors instead:
>
>      xray_data {
>        file_name = "data_withoutI.mtz"
>        labels = "F,SIGF"
>        r_free_flags {
>          file_name = "data_withoutI.mtz"
>          label = "FreeR_flag"
>          test_flag_value = 0
>        }
>      }
>
> then this seems to be the right ballpark for a 1.75 Angstrom structure....
>
> | maximum likelihood estimate for coordinate error:   0.28 A
>
> Similar R-factors, but there is a factor of 10 difference in the scale 
> reported here:
>
> I's:
> r_work= 0.2266 r_free= 0.2570 ksol= 0.41 Bsol= 50.00 scale= 0.097
> F's:
> r_work= 0.2221 r_free= 0.2557 ksol= 0.41 Bsol= 50.00 scale= 0.965
>
>
>    Version: 1.4
>    Release tag: 3
>    cctbx tag: 2008_12_07_1353
>    Platform: mac-intel-osx osx-10.5.6
>    User: phil
>
> Cheers,
> Phil Jeffrey
> Princeton
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