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charnley / rmsd

Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format
BSD 2-Clause "Simplified" License
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be aware of reflection operation #76

Closed SingletC closed 3 years ago

SingletC commented 3 years ago

reflection operation would not be aligned after centered or kabsch rotation.

nbehrnd commented 3 years ago

Dear SingletC,

you are welcome to report errors by calculate_rmsd.py's action, issues when using the script in general, etc. To facilitate the replication of your observation(s), consider the addition of a typical set of data leading to the problem encountered. For this purpose, a .zip archive with the .xyz/.pdb files in question read/written by the script is a convenient container to keep them all in one place in common. Contrasting to .xyz/.pdb files, archives in the .zip format are accepted by GitHub's interface of discussion, too.

Please note, because e-mail attachments typically do not pass and enter GitHub's interface of discussion, this edit requires a running session in GitHub.

charnley commented 3 years ago

@SingletC, The reflection function is only used as an approximation to finding the atom-pairs coupled with a reorder_method, before rotation.

Do you have a specific example where alignment fails?

SingletC commented 3 years ago

I got it now, Thanks