[phenixbb] phenix xtriage

Pavel Afonine PAfonine at lbl.gov
Mon Apr 20 21:00:11 PDT 2009


Hi Peter,

what does "score: a likelihood based score combining all info" exactly 
mean? What is the "good value" (and why), what is "so-so value", and 
what is the "bad value" (and why)? Could you please give a reference to 
where this score is defined and its use is evaluated?

I asked myself all these questions when I read this phrase in your reply 
below and, sorry for my ignorance, I failed to find the answers.

Thanks!
Pavel.


On 4/20/09 12:06 PM, Peter Zwart wrote:
> 2009/4/20  <sbiswas2 at ncsu.edu>:
>   
>> Hi,
>>
>> I tried running phenix xtriage with a scaled data in P4322 space group. I
>> got the following output:
>> -----------------------------------------------------------------------------------
>> | space group | n absent | <Z>_absent | <Z/sigZ>_absent | +++ | --- |
>> score       |
>> -----------------------------------------------------------------------------------
>> | P 4 2 2     | 0        |     0.00   |     0.00        |  0  |  5  |
>> 0.000e+00  |
>> | P 41 2 2    | 0        |     0.00   |     0.00        |  0  |  5  |
>> 0.000e+00  |
>> | P 42 2 2    | 0        |     0.00   |     0.00        |  0  |  5  |
>> 0.000e+00  |
>> | P 43 2 2    | 0        |     0.00   |     0.00        |  0  |  5  |
>> 0.000e+00  |
>> | P 4 21 2    | 8        |     1.71   |     8.07        |  6  |  3  |
>> 4.817e+00  |
>> | P 41 21 2   | 8        |     1.71   |     8.07        |  6  |  3  |
>> 4.817e+00  |
>> | P 42 21 2   | 8        |     1.71   |     8.07        |  6  |  3  |
>> 4.817e+00  |
>> | P 43 21 2   | 8        |     1.71   |     8.07        |  6  |  3  |
>> 4.817e+00  |
>>
>> Can anyone explain what these numbers mean? It seems all enantiomorphic
>> space groups have the same score (which is the last column)
>>     
>
> n absent: number of absent intensities according to spacegroup
>
> Z absent: mean normalized intensity for absent reflections
> Z/sigZ: 'signal to noise' of absent reflections
> +++ : reflections that seem present that should be absent
> ---- : reflections that seem absent but should be present
> score: a likelihood based score combining all info
>
> If you want, you can send me your sca file and I can have look to make
> sure that nothing is messed up.
>
> Cheers
>
> Peter
>
>
>   
>> The documentation in phenix does not explain this in detail.
>> I scaled the data in HKL2000 and there was no systematic absences with
>> P43222.
>> Thanks,
>> Shya
>>
>>
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>>
>>     
>
>
>
>   
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