Hello Jiayi
I have used this before, but do not remember the details.
To me, paired list meand one atom from each model. The xample in the
documentation also looks like that.
Also, the simple numbers are not good for atom numbers; they mean
residue numbers in proteins or nucleic acids (see "atom expressions"
in the doc).
I suggest trying
compare {1.1} {2.1} SUBSET {*} ATOMS {atomno=1} {atomno=2} {atomno=2}
{atomno=3} {atomno=3} {atomno=4} {atomno=4} {atomno=1} rotate
translate 2
You may possibly use the shorthand notation for atom numbers:
compare {1.1} {2.1} SUBSET {*} ATOMS {@1} {@2} {@2} {@3} {@3} {@4}
{@4} {@1} rotate translate 2
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