From 819ca80eeb614712db14aabf9320a917f268b8e7 Mon Sep 17 00:00:00 2001 From: "Jimmy C. Kromann" Date: Mon, 2 Dec 2024 15:45:06 +0100 Subject: [PATCH] Update README.rst --- README.rst | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index 316f620..f00e54f 100644 --- a/README.rst +++ b/README.rst @@ -14,11 +14,10 @@ For more information please read RMSD_ and `Kabsch algorithm`_. Motivation ========== -You have molecule A and B and want to calculate the structural difference -between those two. If you just calculate the RMSD_ straight-forward you might -get a too big of a value as seen below. You would need to first recenter the -two molecules and then rotate them unto each other to get the true minimal -RMSD. This is what this script does. +I want to know the minimal RMSD between two molecules +----------------------------------------------------- + +You have two molecules, A and B, and want to calculate the structural difference between them. If you just calculate the RMSD straight-forward, you might get too big a value, as seen below. You need to recenter and rotate the two molecules to get the true minimal RMSD. This is what this code does. ========== =========== ========== No Changes Re-centered Rotated @@ -33,6 +32,14 @@ RMSD 2.50 RMSD 1.07 RMSD 0.25 .. |rotate| image:: https://raw.githubusercontent.com/charnley/rmsd/master/img/plot_rotated.png +I do not know the order of the atoms +------------------------------------ + +If atoms in molecules A and B are not in the same order, you will need to reorder the atoms first to get the correct rotation for minimal RMSD. + +.... + + Citation ========