PyMOL's Secret Weapon: Master Atom Positioning!

Selections in pymol are sets of atoms and are differentiated from objects by the use of ( ) in the object control menu. The default selection is (sele) which is automatically created upon. Pymol select command is described in detail here: In your case, to select certain atom. Conceptually, pymol atom selections are simply lists of atoms.

If you wish to use a. Get_position gets the 3d coordinates of the center of the viewer window. Atom selection in pymol to the corresponding line in a pdb file. To print out the coordinates within pymol, you need to use the command iterate_state, e. g. : There are several ways to extract or load atomic coordinates in pymol using the python api.