XYZ files do not include bond information, while MOL and MOL2 do.
So I guess your C--P distances are above what Jmol considers "bonded"
Maybe you can change the default value of
set bondTolerance (decimal)
"When autobonding, the value of bondTolerance is added to the two bond
radii of atoms being tested for a bond. A larger bondTolerance allows atoms
that are further apart than the sum of their listed radii to still be bonded.
This
parameter should be adjusted prior to file loading for proper maintaining of
the Jmol state."
Other possible ways to fix that:
{_P}.bondingRadius =
set bondingVersion
data "element_vdw" 6 1.7; 7 1.8 END "element_vdw"
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