alignment - Aligning 2 small molecules in PyMOL -


i want align ligands in pymol 1 protein structures, error message:

executivealign: mobile selection must derive 1 object only

i copied ligands separate pdb files, renamed hetatm entries atom, still error. wondering why pymol has problems aligning small molecules.

ps: ligands have similar structure, different coordinates.

when align align function pymol seeds structural alignment doing sequence alignment first.

you can use pair_fit function have specify corespondency between atoms. function takes 2 selections, 1 each element, have same number of atoms.

if ligands have exact same chemical structure can pass objects directly, if not have make appropriate selections.


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