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2024-05-02T17:45:37Z

asdf

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	[[Category:SEA]]		[[Category:SEA]]
			[[Category:Curator]]
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Frodo at 05:10, 14 February 2014

2014-02-14T05:10:51Z

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	[prompt]$ sea-fit -c cutoff model.out		[prompt]$ sea-fit -c cutoff model.out

			[[Category:SEA]]

Frodo: 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..."

2012-10-11T23:15:19Z

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..."

New page

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

Generate model - Revision history

Frodo: asdf

Frodo at 05:10, 14 February 2014

Frodo: 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..."