How big is the box? Is the COR2 segment centered in the middle of the box? Is each MACR residue a whole molecule? Or is each molecule in the MACR segment composed of multiple (e.g. 4) residues?

The value 53.0 is a fairly large cutoff distance for the .around. operator, esp. to characterize interactions.

The .byres. operator will not select a whole molecule if some of the residues in the molecule are outside the other criteria (.around. and prop Z), so you may need additional selections that utilize the .bonded. operator to get the whole molecules.

Ideally, whole molecules are either residues or segments; a segment with many multiple residue molecules poses distinct challenges fro atom selection.


Rick Venable
computational chemist