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 to the RMSD between the first conformer and the other conformers. The RMSD between any two conformers can also be calculated (shown in the example). Also, if you just want to compute the RMSD values without aligning the conformers (e.g. if conformers are already aligned), you can disable alignment via the prealigned flag in the function. Example using the function can be found here: https://www.rdkit.org/docs/GettingStartedInPython.html#working-with-3d-molecules
"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?). " As far as I know, if two conformers (superimposed) have an RMSD > 0, then they are different. However, for most applications, conformers with low RMSD value (e.g. < 0.5) are considered redundant and hence only one is retained, because they will usually give similar results in calculations as their geometry is very similar. Depending on the application and degree of conformational diversity required, the RMSD cutoff for considering two conformers redundant varies. I hope this helps. Best regards, Omar On Thu, Oct 17, 2019 at 10:01 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 >
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