[phenixbb] amazing good statistics

[Simon Kolstoe]

Is there an equivalent of phenix.r_factor_statistics for other parameters like RMSD bond angles/lengths? I note you can get histograms in the GUI version of polygon but only when you input a pdb file for validation.

Thanks,

Simon


On 3 Apr 2012, at 18:41, Pavel Afonine wrote:

> Hi Christian,
> 
> this is kind of Rwork/Rfree that you would get if you take a very high resolution structure, may be 1.2-1A and higher, cut the data off at 2.2A, and refine it again.
> So one explanation is that your crystals could probably diffract to a higher resolution...
> 
> The command
> 
> phenix.r_factor_statistics 2.2
> 
> gives typical R-factors at around 2.2A resolution are:
> 
> Histogram of Rwork for models in PDB at resolution 2.10-2.30 A:
>     0.115 - 0.137      : 9 <<< you are here
>     0.137 - 0.159      : 121
>     0.159 - 0.182      : 703
>     0.182 - 0.204      : 1637
>     0.204 - 0.226      : 1749
>     0.226 - 0.248      : 735
>     0.248 - 0.270      : 147
>     0.270 - 0.293      : 12
>     0.293 - 0.315      : 2
>     0.315 - 0.337      : 2
> Histogram of Rfree for models in PDB at resolution 2.10-2.30 A:
>     0.157 - 0.181      : 20 <<< you are here
>     0.181 - 0.205      : 163
>     0.205 - 0.229      : 784
>     0.229 - 0.253      : 1733
>     0.253 - 0.277      : 1617
>     0.277 - 0.301      : 671
>     0.301 - 0.325      : 101
>     0.325 - 0.349      : 22
>     0.349 - 0.373      : 5
>     0.373 - 0.397      : 1
> Histogram of Rfree-Rwork for all model in PDB at resolution 2.10-2.30 A:
>     0.001 - 0.011      : 47
>     0.011 - 0.021      : 176
>     0.021 - 0.031      : 533
>     0.031 - 0.041      : 997 <<< you are here
>     0.041 - 0.050      : 1306
>     0.050 - 0.060      : 1062
>     0.060 - 0.070      : 602
>     0.070 - 0.080      : 216
>     0.080 - 0.090      : 113
>     0.090 - 0.100      : 65
> Number of structures considered: 5117
> 
> Pavel
> 
> 
> On 4/3/12 9:59 AM, Christian Roth wrote:
>> Dear Phenix people,
>> 
>> is there a major improvement in the algorithm? I have refined a 2.2 Ang. room
>> temperature dataset with very good data statistics (I think)
>> Rmerge  3.7%(8.9%)
>> completeness  96%(92%)
>> I/sigI  16,6(8,8)
>> in parentheses are the values for the highest resolution shell.
>> 
>> After refinement I have a R/Rfree of 0.1294/0.1670.
>> In some shells there are values close to 0.100 and in the lowest shell Rfree
>> is lower than Rwork.
>> The quality of the data are really quite good, what is probably one of the
>> reasons,  but I am close or below to the border of the Range of R values in
>> the pdb. Great for me, but I wanna be sure that it is really true.
>> It was a MolRep with a close homolog, but I run a torsion angle sim annealing
>> to decouple R/Rfree and the MolRep was done with an poly-Ala model to prevent
>> too much model bias.
>> 
>> Best Regards
>> 
>> Christian
>> 
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