Analyzing the anomalous signal in a SAD dataset with anomalous_signal

Author(s)

Purpose

anomalous_signal is a tool for estimating the anomalous signal in a SAD experiment and for predicting whether this signal is sufficient to solve the structure. This tool normally is used in combination with plan_sad_experiment (planning the experiment) and scale_and_merge (scaling the unmerged data and also obtaining two half-datasets).

Usage

How anomalous_signal works:

Output from anomalous_signal

anomalous_signal provides a summary of the skew, measurement error, and half-dataset correlations in your dataset and the estimated anomalous signal, probability of solving the structure and estimated figure of merit of phasing. Here is an example:

-------------------Summary of signal in this dataset ------------------------


       Shell

                       CCano   Nrefl Nrefl
Resolution Esqr I/sigI  half   anom   half
48.2- 6.0  0.09  33.09  0.85    2090  2032
 6.0- 5.5  0.34  23.31  0.53     667   659
 5.5- 5.0  0.34  22.84  0.49     956   947
 5.0- 4.5  0.28  29.23  0.38    1468  1447
 4.5- 4.0  0.42  24.00  0.16    2305  2276
 4.0- 3.5  0.57  14.02  0.05    3832  3751
 3.5- 3.0  0.84   5.91  0.01    6869  6494
 3.0- 2.9  1.52   2.39  0.00    2035  1734

       Cumulative


----------------------Data quality-----------------    Best guess of expected
                                                      results of finding sites
                                                     ------ and phasing--------

                     CCano   Nrefl                    P(Substr)
Resolution Skew Esqr  half   anom    CC* Signal  +/-     (%)       FOM*  +/-
48.2- 6.0  0.03 0.08  0.85    2090  0.71   6.3   0.4      23       0.3   0.1
48.2- 5.5  0.02 0.10  0.82    2757  0.76   7.8   0.3      40       0.3   0.1
48.2- 5.0  0.01 0.12  0.78    3713  0.70   8.3   0.6      47       0.3   0.1
48.2- 4.5  0.03 0.14  0.72    5181  0.68   9.5   0.7      61       0.3   0.1
48.2- 4.0  0.03 0.17  0.62    7486  0.72  12.1   0.6      76       0.4   0.0
48.2- 3.5  0.02 0.25  0.43   11318  0.66  13.6   1.4      83       0.4   0.0
48.2- 3.0  0.00 0.47  0.24   18187  0.48  12.7   2.0      79       0.3   0.1
48.2- 2.9  0.00 0.59  0.22   20222  0.42  11.8   1.7      74       0.3   0.1

Notes:
Skew is skew of origin-removed anomalous difference Patterson
Esqr is the squared ratio of sigmas to differences:<SigAno**2>/<Dano**2>
I/sigI is the mean value of (Ihkl/sigIhkl)
CCano half is the correlation between half-dataset anomalous differences
Nrefl half is the number of anomalous differences in both half-datasets
Nrefl anom is the number of anomalous differences in the entire dataset
CC* is estimate of anomalous correlation to ideal data
Signal +/- sigma is estimate of anomalous signal (peak height at coordinates of
anomalously-scattering atoms in difference Fourier phased with model
phases.)

Note that the anomalous signal increases with the square root of the
number of reflections and decreases with the square root of the number
of sites.

P(Substr) is estimate of probability that the sub-structure can be found
with LLG-based HySS and this data.
FOM* +/- sigma is estimate of phasing FOM if sub-structure is solved

Possible Problems

anomalous_signal assumes that your crystal is similar to others that have been solved. If your crystal has serious decay or other factors that reduce signal to noise, the estimates provided by plan_sad_experiment may be too optimistic.

Literature

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