load files "$tyrosine" "$lysergamide" select 2.1; translateSelected {10 0 0} frame *;zoomto 0 {*} 0 select {2.1} wireframe only display remove 1.1 and _H delay 1 // use a SMARTS string to find the key atoms in both molecules sm = "c1ccccc1CCN" keyatoms = {*}.find(sm) select keyatoms selectionHalos on // optional way to get dihedral lists based on SMARTS //print {1.1}.find(sm, "BONDS") // get an array of numbers indicating the dihedrals, their current values, and their target values based on a SMARTS match. x = compare({1.1},{2.1},sm,"BONDS") // rotate using a new option to rotate a whole series of dihedrals concurrently rotate branch @x 1 // overlay one model on another with a fit based on the same SMARTS match compare {1.1} {2.1} SMARTS @sm rotate translate // fly in to the model zoomto 1 {*} 0 // new distance option -- minimum distances to another atom set {1.1}.property_d = {1.1}.distance.min({2.1}) select {1.1} color balls property_d select {1.1 and keyatoms} set echo top echo tyrosine colored by distance |to lysergamide