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Pseudo atom in a cavity

Hi there,

I want to place a pseudo atom in a cavity in PyMol. There is a small opening through which a ligand can enter and I want to place a pseudo atom at the centre of this opening. Anyone did this kind of thing?

pymol python protein
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updated by Biostar 380 • | written by Kanika 1

These tools do not place atom at the void. Pseudo atom in PyMol places this at specific coordinates or at a residue. The question is about placing the atom in void by first finding the coordinates of void.

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written by Kanika 1

If you already know the atoms of the opening of the cavity, then select and create a new object (obj1) from action menu. Then place a pseudoatom by 

pseudoatom StartCavity, obj1
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written by dasdevashishdas 12

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