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 situation you are in.
-P. On Thu, Oct 17, 2019 at 3:01 PM Stamatia Zavitsanou < stamatia.zavitsa...@oriel.ox.ac.uk> wrote: > 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 molecules. Is > that correct? If the two conformations do not differ a lot the RMSD should > be low ( if lower than 1A, then the two conformations don't really differ, > is that also correct?). > > Will the code translate and rotate the molecules in order to get the > perfect alignment or does it just place the one on top of the other? > > What is the difference with GetBestRMS function since the AlignMol is > supposed to give me the minimum RMSD? > > Many thanks, > > Stamatia Zavitsanou > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- -P. Sent from a cell phone. Pls forgive brvty and m1$tea@ks.
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