Comments (2)
Will take a look (reference to #102 )
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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
*:
$ 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.
from rmsd.
Related Issues (20)
- msg = f"error: Parsing atomtype for the following line:" f" \n{line}" HOT 10
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- saving rotated coordinate? HOT 2
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- error: Structures not same size HOT 3
- Incorrect values for proteins HOT 5
- error: Structures not same size HOT 4
- reordering while preparing for output HOT 4
- rmsd package requires typing_extensions but missing from setup.py HOT 1
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- Why these two pdbs can not calculate RMSD? HOT 4
- How to get full transformation in a script? HOT 1
- RMSD result using --reorder much higher than expected HOT 5
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from rmsd.