Pseudo atom in a cavity

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7.2 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 • 2.1k views

ADD COMMENT • link updated 6.4 years ago by Biostar 20 • written 7.2 years ago by Kanika ▴ 10

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There are many tools in a single link

http://www.caver.cz/index.php?sid=133

Pseudoatom:

https://pymolwiki.org/index.php/Pseudoatom

GUI-tool:

https://pymolwiki.org/index.php/Bnitools

Sticks:

https://sourceforge.net/p/pymol/mailman/message/18962925/

ADD REPLY • link 7.2 years ago by natasha.sernova ★ 4.0k

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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.

ADD REPLY • link 7.2 years ago by Kanika ▴ 10

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You appear to have asked this on ResearchGate?

Has the issue been resolved?

ADD REPLY • link 6.4 years ago by Kevin Blighe 87k

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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

ADD REPLY • link 6.4 years ago by dasdevashishdas ▴ 120

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