core rmsd in coot

From: Ursula Schulze-Gahmen
Date: 3 April 2012 21:51
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

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From: Paul Emsley

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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From: Eleanor Dodson
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

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Professor Eleanor Dodson

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From: Ed Pozharski

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?

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"I'd jump in myself, if I weren't so good at whistling."
                              Julian, King of Lemurs