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
