Re: [Rdkit-discuss] AlignMol and GetBestRMS

[Paolo T. <pao...@gm...>]

Hi Stamatia,

the difference between GetBestRMS and AlignMol is that GeBestRMS will 
yield the lowest RMSD across all symmetry-equivalent supeirmpositions, 
whereas AlignMol will yield the RMS from a single superimposition, by 
default obtained overlaying atoms with the same index across the two 
conformations.

See this gist for an example:

http://htmlpreview.github.io/?https://gist.githubusercontent.com/ptosco/967ed3739cdcb169cf8308502f9c5881/raw/60e20790b1a78f88abfe348029c2134f8273a9c3/GetBestRMS.html

Cheers,
p.

On 10/17/19 16:36, Stamatia Zavitsanou wrote:
> What is the difference with GetBestRMS function since the AlignMol is 
> supposed to give me the minimum RMSD?