# [phenixbb] phenix xtriage

Peter Zwart phzwart at gmail.com
Mon Apr 20 23:34:10 PDT 2009

Hi Pavel,

Normalized intensity is normalized as usual (includes epsilon weights): <Z> = 1.

When a reflection is classified as absent due to the space group, its
ideal value should be zero. Any deviation from zero would be due to
experimental error.  If a reflection is not absent, one expects that
this intensity would be drawn from a Wilson like distribution (either
centric or acentric), depending on the symmetry.

The 'error' free value of the intensity responsible for the
observation, is thus either 0 (when absent) or drawn from a Wilson
distribution. The 'score' for a single observation (depending on the
space group),  is then (for an observed intensity)

- int_0^\infty log[p(z |  z_obs, sigma_z)]*p(z| wilson) d z

with p(z |  z_obs, sigma_z) conveniently designated as a Gaussian

The best score is used as a base line, and the best scapcegroup will
always be zero.
Strictly speaking, a score of 4.8 for P43212 indicates that P422 (with
score 0) is about 120 (exp[score]) times more likely. Realistically,
the order is more important and can be used to prioritize MR or HA
searches if need be.
Also, when no absence information is present (missing data) all space
groups will have the same score. It provides a hassle free way to rank
possible space group on the basis of the associated implications for
intensity statistics.

Below you will find a table with scores for a single reflection with
observed normalized intensity in the first column (Z), its score when
it is acentric, centric or absent. In all cases, sigma was 0.5. Lower
score indicate a more likely choice. In this case, an observed value
of 0.5 indicates that the reflection is more likely to be centric then
absent. If z would be 0.4, it would be more likely that it would be an
absent reflection.

Z    acen cen  absent  z/sigz
0.00 1.00 0.67 0.23 0.00
0.05 0.94 0.64 0.23 0.10
0.10 0.89 0.61 0.25 0.20
0.15 0.84 0.59 0.27 0.30
0.20 0.80 0.58 0.31 0.40
0.25 0.77 0.57 0.35 0.50
0.30 0.74 0.58 0.41 0.60
0.35 0.72 0.58 0.47 0.70
0.40 0.70 0.60 0.55 0.80
0.45 0.69 0.62 0.63 0.90
0.50 0.68 0.65 0.73 1.00
0.55 0.69 0.68 0.83 1.10
0.60 0.69 0.71 0.95 1.20
0.65 0.70 0.75 1.07 1.30
0.70 0.72 0.79 1.21 1.40
0.75 0.73 0.84 1.35 1.50
0.80 0.76 0.89 1.51 1.60
0.85 0.79 0.94 1.67 1.70
0.90 0.82 1.00 1.85 1.80
0.95 0.85 1.06 2.03 1.90
1.00 0.89 1.12 2.23 2.00

The total score for a space group is based on the different
classifications for the miller indices.
I have found this scheme to be more reliable then plain i/sigi
considerations, as it takes into account differences between centric
vs acentric. Furthermore, no special precautions need to be taken for
missing data, nor do I need to worry about completion issues when
usnig FFT based approaches.

> "bad value" (and why)? Could you please give a reference to where this score
> is defined and its use is evaluated?
>
> below and, sorry for my ignorance, I failed to find the answers.

Not a surprise, this still needs to be published.

HTH

Peter

--
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P.H. Zwart
Beamline Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:     http://bcsb.als.lbl.gov
PHENIX: http://www.phenix-online.org
CCTBX:  http://cctbx.sf.net
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