Heavy-atom search

The heavy-atom search procedure of CNS can be applied to various native and difference Patterson maps and their statistically weighted averages. Using the default parameters, a search for two thirds of the number of expected sites is often successful. In the example, 100 trials are carried out, searching for 6 of the expected 9 sites. 
      cns_solve < heavy_search.inp > heavy_search.out  [49 minutes]
The beginning of the output file heavy_search.summary should be looked at to check the input parameters. The 100 heavy-atom configurations found are stored in the files heavy_search_*.sdb. A list of trial numbers and correlation coefficients can be found in the file heavy_search.list. Often it is useful to plot the list:

In many cases there are only a few outstanding correlation coefficients, and the highest one normally corresponds to the correct heavy-atom configuration. However, in the example the correct configuration was found many times.

On Unix computers, the list file can easily be sorted. 

      sort +1n -r heavy_search.list
The beginning of the output shows that heavy_search_1.sdb is one of the correct configurations. 
       +1     0.5279
      +15     0.5279
      +17     0.5279
       +6     0.5279
      +79     0.5279
       +9     0.5279
      +10     0.5278
      +12     0.5278
      +13     0.5278
       +2     0.5278
      +29     0.5278
      +48     0.5278
      +61     0.5278
       73     0.5001
       83     0.5000
       95     0.4937
       ...
To aid the interpretation of the distribution of the correlation coefficients, trials with a correlation coefficients greater than 1.5 sigma of all trials are flagged with a plus sign.

The configuration corresponding to the top of the sorted list, heavy_search_1.sdb, can be used in the predict_patterson.inp task file for visual comparison of the observed and calculated Patterson maps (see previous tutorial), and as input for refinement of the heavy-atom parameters and computation of experimental phases (see following tutorials).

Script to run this tutorial

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