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 3 sites. 
      cns_solve < heavy_search.inp > heavy_search.out  [8.5 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. In this example the highest correlation coefficient is seen for the first 3 trials.

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 0.5589
       +2 0.5589
       +3 0.5589
       51 0.4353
        8 0.4353
       68 0.4352
       47 0.4230
       16 0.4130
       ...
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 best configuration corresponding, heavy_search.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 in the ir_phase.inp task file for refinement of the heavy-atom parameters and computation of experimental phases (see following tutorials).

Script to run this tutorial

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