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
(I meant an RMSD of about 1 Angstrom. )
On Thu, Oct 17, 2019 at 5:00 PM Peter S. Shenkin wrote:
> A large RMSD could come about from a large number of small interatomic
> deviations or a small number of large ones. In the latter case, the
> difference in conformation could be large. It is useful
A large RMSD could come about from a large number of small interatomic
deviations or a small number of large ones. In the latter case, the
difference in conformation could be large. It is useful to also obtain the
largest interatomic deviation following superimposition in order to
determine which s
Dear Stamatia,
If you have conformations of the same molecule and want to align them or
just compute RMSD between them , I think you should use the
AlignMolConformers function. This function will align all conformers of a
mol on the first conformer, and returns a list of RMSD values corresponding
Hello all,
I have been using the AlignMol function to get the difference in RMSD between
the different conformations of a molecule. (the conformations are generated by
another software). As I understand the the code will return the minimum RMSD
and therefor the best way to align the two molecu
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