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On 16/07/15 14:04, cedric bauvois wrote: > Sorry if it was not clear, > > Maybe, it will be easier to understand with the example of the > mechanism of action of b-lactam (probably not the best example but > well known). > > http://proteopedia.org/wiki/index.php/Sandbox_126 > Beta-Lactam (β-Lactam) antibiotics, which include penicillins, > cephalosporins and carbapenems, bind and irreversibly inhibit > transpeptidases by mimicking the D-Ala-D-Ala moiety, resulting in the > inhibition of cell wall synthesis and ultimately bacterial cell growth. > > for an illustration in 2D, see > http://proteopedia.org/wiki/index.php/Image:DalMimic.jpg > > In our case, we are working with a small organic compound that mimicks > a small part of a three turn a-helix peptide and we would be > interested to find the best way to superimpose them both. > > hoping it will help the understanding. > > Yes, it does (for me). The problem as it stands is tricky because you are matching a single "residue" onto several - I don't know of any means to do that. If you can describe your protein fragment as a single "residue" (you will have to change the atom names for some atoms) then you can use overlap-ligands and match-ligands-torsion functions in coot. You can find a clicky-clicky interface for that here: http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/enhanced-ligand.scm Paul.