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@oyileo Because the two structures differ in atom count (either in the form shared by you, or neglecting hydrogen atoms), calculate_rmsd is going to report "structures of different size", and exit.
For one, 8gxn.pdb is about a structure model including hydrogen atoms. Counting the atoms with openbabel and wc -l*:
For two, 8gxo.pdb is about a model without any hydrogen atoms. Its number of atoms differs to the one in 8gxn.pdb, and a deletion of hydrogens in 8gxn.pdb alone is not sufficient for an analysis by calculate_rmsd:
$ obabel 8gxo.pdb -oxyz | wc -l
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is 8gxo.pdb)
1 molecule converted
4001
$ obabel 8gxo.pdb -oxyz | grep "H" -c
==============================
*** Open Babel Warning in PerceiveBondOrders
Failed to kekulize aromatic bonds in OBMol::PerceiveBondOrders (title is 8gxo.pdb)
1 molecule converted
0
* The count is off by two (the line about the number of atoms, the line of optional comments), but this systematic error will be present in both checks.
pdb: 8xgo 8xgn
CsFAOMT.zip
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