I wish Paul, that at least SOME of the great info that coot prints to the
screen then scrolls out of sight could be directed to a
"very-useful-things-to-remember" box..
Eleanor
On Apr 4 2012, Paul Emsley wrote:
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.
--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266
