Hi All,

I've been using the "Align Molecules using Substructure" component to align libraries of compounds using the MCSS as the substructure.  The protocol I wrote gives the user the opportunity to tweak the orientation of the MCSS, in the event that the user has a specific orientation that they'd prefer the molecules to have.

My experience with this component has been a little spotty. Sometimes it fails to align at all and it never rotates bonds to reflect the preferred orientation of the molecule.  Does anybody have a solution to this problem?  For rigid compounds this component works great, but it appears that as soon as a molecule gets a few rotatable bonds, the alignments don't seem to work as well.  Any advice is appreciated!  I'm working within the confines of PP 7.5 for now, so I'm not sure if this has already been addressed in later versions.

Many thanks,

Scott