RMSD on alpha-carbon

[yazdan12555]

Hi.
Does the code have the ability to run RMSD only on alpha carbons?
i couldn't find a related option by running "calculate_rmsd --help"

[charnley]

The feature is not available using the command line interface. However,

A) you can read the PDB with Python and use the functions from the library

B) Remove all other atoms from the PDB file and use the command line interface

If it is a feature you need, you are welcome to open an issue.

[yazdan12555]

Hi Jimmy,

Thanks so very much for the quick response. I got my answer from your suggestion :)

Best,

Yazdan

[charnley]

You can now call calculate_rmsd with --only-alpha-carbons

calculate_rmsd --only-alpha-carbons file1.pdb file2.pdb

and if the the atoms are not in the right corner, you can call it with --reorder

calculate_rmsd --reorder --reorder-method qml --only-alpha-carbons file1.pdb file2.pdb

[yazdan12555]

Excellent! Thanks so very much.