[phenixbb] clashscore discrepancies

[Jeff Headd]

Hi Alex,

While small discrepancies would not be surprising, 2.57 vs. 4.2 is quite
different, and indicative that something is not working correctly. Would
you be willing to send me the PDB file (offline) from phenix.refine that
reports a clashscore of 2.57 so I can look into the behavior directly?

Thanks,
Jeff


On Sat, Apr 27, 2013 at 7:21 PM, Alex Theodossis <alex.theodossis at monash.edu
> wrote:

> Dear phenixbb,
>
> I have carried out refinement using the latest version of PHENIX, which
> gives improved molprobity stats. However, these stats still do not match
> those porvided by the molprobity server:
>
>
>                                    PHENIX output
>         Molprobity server
>
>  Existing H-model           Electron-cloud  H-model
> All atom clashscore             2.57                           4.2 (81st
> perc)                 3.25 (88th percentile)
> Rotamer outliers                   0.7                              1.14
>                                   1.14
> Overall score                      1.04                         1/24 (89th
> perc)                   1.16 (93rd percentile)
>
>
> Given that PHENIX is now giving me the best results and all scenarios give
> reasonable results I am less inclined to be concerned. However, I still
> find these inconsistencies rather puzzling and am curious to learn what is
> causing them.
>
> Thanks in advance.
>
>
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>
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