Comments (2)
Hey, I would say RMSD can be different by design, rna_calc_rmsd.py, reads atoms in given order, so if you rpr your structure and standardzie the atom order, so if the atom order in the original file is different, then the rmsd will be non zero because different atoms will be used for calculations.
The best way is to always rpr both files to make sure that you have the exact order of atoms (I should maybe do it automatically inside to the rna_calc_rmsd.py tool, and add an option not to rpr models automatically, I've been thinking about it)
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Thanks for the clarification. This explains the discrepancies.
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