As a follow up question on this topic, I would like to ask if
MurckoScaffold.GetScaffoldForMol(mol) returns the scaffold of mol with
different coordinates?
I am asking this because when I use the transformation matrix of the
alignment of the cores of the probe and the reference molecules, in order
to align the whole probe to the reference molecule, the two molecules don't
seem to be aligned (they are in distance). Basically I do this:

qcore = MurckoScaffold.GetScaffoldForMol(qmol)
refcore = MurckoScaffold.GetScaffoldForMol(refmol)
pyO3A = rdMolAlign.GetO3A(qcore, refcore, prbCid=qconfID, refCid=0,
reflect=True)
AllChem.TransformMol(qmol, bestRMSDTrans[1], confId=bestconfID,
keepConfs=False)

and then I write the qmol in an sdf file. But when I visualize it the qmol
is far from the refmol!





On 20 February 2017 at 02:33, Thomas Evangelidis <teva...@gmail.com> wrote:

> Dear all,
>
> I want to align 250 compounds that binding to the same pocket to one of
> the 9 available crystal ligands. I chose the reference ligand based on the
> Morgan2 similarity to the probe molecule. Then I align the 2 compounds
> using:
>
> pyO3A = rdMolAlign.GetO3A(qmol, refmol, prbCid=qconfID, refCid=0,
> reflect=True)
> RMSD = pyO3A.Align()
>
> ​and keep only the conformer of the probe with the lowest RMSD to the
> reference compound. However, the alignment looks terrible when I visualize
> it, so I would like to ask if there is any way to align the maximum common
> substructure only. I tried to align only the core of both molecules as
> defined by MurckoScaffold.GetScaffoldForMol(mol)​, but still the
> alignment looks bad. I have seen in the documentation how to find the
> maximum common substructure with rdFMCS.FindMCS but before I engage into
> programming it I would like to know if there is any automatic way to find
> it on the fly while aligning the 2 molecules.
>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> Research Specialist
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/1S081,
> 62500 Brno, Czech Republic
>
> email: tev...@pharm.uoa.gr
>
>           teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
>


-- 

======================================================================

Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

email: tev...@pharm.uoa.gr

          teva...@gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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