Re: [ccp4bb] core rmsd in coot
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.
Re: [ccp4bb] core rmsd in coot
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
Re: [ccp4bb] core rmsd in coot
On Wed, 2012-04-04 at 17:31 +0100, Eleanor Dodson wrote: 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 Won't coot | tee very_useful_things_to_remember.txt do just that? -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
[ccp4bb] core rmsd in coot
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? Yrsyla -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220
