(I meant an RMSD of about 1 Angstrom. ) On Thu, Oct 17, 2019 at 5:00 PM Peter S. Shenkin <shen...@gmail.com> 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 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$tea@ks. > -- -P. Sent from a cell phone. Pls forgive brvty and m1$tea@ks.
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