RMSD error in PyMol ?

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Kangkon Saikia

Specify the amino acid region common in both the protein and try carrying out the alignment.

Or you can use VMD for this purpose, which is very easy to use.

Prabhat Neupane

Thank you so much for the information.

Abu Turab Naqvi

What command exactly did you use? Also it will be helpful if you share the input files.