How to calculate the distance from a pocket to a specific residue in the protein?

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Andrew Orry

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Jan 13, 2023, 1:22:27 PM1/13/23
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Q.  I have calculated pockets using ICMPocketFinder. How to calculate the distance from a pocket to a specific residue in the protein?

A.
Use the commands shown below where g_pocket_rec1 is your pocket and K132 is the residue in object a_rec.a

# distance between grob center and center of some resodue

Distance( Mean(Xyz(g_pocket_rec1 )) Mean(Xyz(a_rec.a/^K132/)))   

# distance between grob center and specific atom
Distance( Mean(Xyz(g_pocket_rec1 ))Rarray(Xyz(a_rec.a/^K132/ca)))  


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