Pseudo atom in a cavity
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4.7 years ago
Kanika ▴ 10

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 • 1.4k views
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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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You appear to have asked this on ResearchGate?

Has the issue been resolved?

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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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