Generate model: Difference between revisions
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(Created page with "This is intended for Shoichet lab setup. But we hope other find it useful. See SEA == How to generate a model to run SEA == We need the files: reference.smi ; referenc...") |
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[prompt]$ sea-fit -c cutoff model.out | [prompt]$ sea-fit -c cutoff model.out | ||
[[Category:SEA]] |
Revision as of 05:10, 14 February 2014
This is intended for Shoichet lab setup. But we hope other find it useful. See SEA
How to generate a model to run SEA
We need the files: reference.smi ; reference.set ; reference.fp
First we need to generate the background Z-score distribution:
[prompt]$ sea-background reference.set.gz
This generated the file model.out
Then we need to fit data the data from this background model and build a fit parameter file:
[prompt]$ sea-fit model.out
This generates the file model.out.distfit, containing the values for the best fit of the background distribution to a normal and an extreme value distribution. From this distribution, we need to select the optimal cutoff (in general we look for the similarity value that better fits to EVD) and then use it to get the fit file.
[prompt]$ sea-fit -c cutoff model.out