Vmd rotate on axis8/18/2023 The coordinates are rotated 90 degrees around the Z axis. Z can be changed to X and Y to rotate around the X and Y axes, respectively. If you want this bond to be parallel to other Cartesian axes, then follow the above method to first make this bond parallel to the X axis and then execute the following code. $sel move Īfter executing the above code, if you want to align bond between atom 3 and 5 to be parallel to the X axis then enter the following codeĪfter that, save the coordinate file. Copy the following code to VMD console and execute. Orient a certain bond parallel to a certain axisįirst load molecule’s structure file (such as.
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