(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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