[phenixbb] phenix xtriage - one more

[Pavel Afonine]

Hi Peter,

one more question... What is "Z absent: mean normalized intensity for 
absent reflections"? I mean:

- what this values is supposed to tell?
- one can normalize things in many various ways. What is the 
normalization procedure in this particular case?

Thanks!
Pavel.


On 4/20/09 9:00 PM, Pavel Afonine wrote:
> 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
>>>
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>     
>>
>>
>>
>>   
> ------------------------------------------------------------------------
>
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