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?
There are many tools in a single link
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.
You appear to have asked this on ResearchGate?
Has the issue been resolved?
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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