I just used PyMol to compare two structures and want to obtain an RMSD value. However, I can only see RMS from the calculation. So I want to know if the RMS is RMSD, or what's the difference.
You can get TMalign within PyMOL: https://pymolwiki.org/index.php/TMalign, module tmalign.py. It is also available part of the PyMOL extension psico https://pymolwiki.org/index.php/Psico