I want to create bonds between e.g. all Pd atoms and all
Si atoms, but only within a specified cutoff radius.
bond (n. pd), (n. si) within 2.5 of (n. pd)
creates all possible bonds between all Pd atoms and all Si
atoms near enough to any Pd atom. This yields a weired
structure with very long, unwanted bonds.
I tried to iterate over the first selection, to draw only
bonds between an Pd atom and Si atoms which are within
range to that Pd atom like
iterate (n. pd), bond id ID, (n. si) within 2.5 of (id
ID)
but get an syntax error. Is it possible to create bonds
within an iteration?
Best regards,
tmartin
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