On 03/04/12 21:51, Ursula Schulze-Gahmen wrote:
When superimposing 2 structures in coot, I get a core rmsd in the
output. What does this mean? Which residues are included in the core
rmsd? Are these all the residues that have equivalent residues in the
moving and reference molecule?
It is the r.m.s.d. (after superposition) of the aligned C-alphas - yes
they have equivalent residues.
The residues are tabulated in the output after:
Moving Reference Distance
Krissinel E, Henrick K
Secondary-structure matching (SSM), a new tool for fast protein
structure alignment in three dimensions
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY 60,
2256-2268, 2004.
http://journals.iucr.org/d/issues/2004/12/01/ba5056/ba5056.pdf (Open
Access)
HTH,
Paul.
