One of many possible ways is to use rms_cur command in pymol.
But fundamentally such number is meaningless, since root mean square deviation is only useful when the average shift between the two structures is (close to) zero.
On 07/23/2012 11:06 AM, Theresa Hsu wrote:
Dear all I have two proteins in PDB each with two subunits. One of the subunits can align well in both. How do I calculate rmsd for the aligned subunits and the other non-align subunits *separately*? Thank you.
