Dear Theresa, You could use Gesamt from CCP4 6.3.0, which will align a given range of residues in one protein onto a range of residues from another protein. Just run $CCP4/bin/gesamt for usage instructions and selection syntax, or use Structure Superposition from CCP4i.
Best, Eugene On 23 Jul 2012, at 16:06, 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. -- Scanned by iCritical.
