errors,Structures not same size

[oyileo]

pdb: 8xgo 8xgn

CsFAOMT.zip

[charnley]

Will take a look (reference to #102 )

[nbehrnd]

@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*:

$ obabel 8gxn.pdb -oxyz | wc -l
1 molecule converted
3934
$ obabel 8gxn.pdb -oxyz | grep "H" -c
1 molecule converted
1846
# tentatively delete hydrogen atoms present
$ obabel 8gxn.pdb -oxyz -d | wc -l
1 molecule converted
2088
$ obabel 8gxn.pdb -oxyz -d | grep "H" -c
1 molecule converted
0

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.