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.
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