Re: [phenixbb] phenix xtriage - one more

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 :

...

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 | _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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