2.1 Input File Preparation

At the minimum, flynn requires a density file and a the connection table of the ligand - usually derived from a supplied molecule file e.q. .pdb, .sdf, .mol2, .smi. Flynn automatically searches the density for volumes of unmodeled density that are similar in size to the input ligand. Because of this it is highly recommended that a protein is also input to flynn. This makes the job of locating the ligand density less prone to false positives.

Based on analyzing several hundred proteinligand combinations, the best way to use flynn for ligand fitting is described as follows (of course your milage may vary):

Always use a protein. The protein is used to identify modeled density where the ligand cannot be placed. Without this, flynn will identify many candidate locations for placing the ligand that will need to be analyzed.
The reflection data should be refined without a previous ligand conformation or generated without the ligand present. While in many cases the same result will be generated, if the ligand is fit to data refined with a previous ligand conformation, flynn may be biased towards the density modified by the pre-existing ligand conformation.

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