Hello, I am using the SMILES input based , ligand coordinate and restraint generation inside coot , which I understand calls libcheck. For some of these ligands , the stereochemistry around parts of the molecule are "wrong" : in that the SMILES string has solid bonds instead of wedges. I am using RDKIT the cheminformatics package to visualize these molecules.
For these SMILES strings the model generated by libcheck inside coot is very mangled. Such that rings circle around and clash with each other for example. For the present moment I am manually editing the molecule to correct the stereochemistry- generate the SMILES string externally and then have libcheck do the right thing. Is there a way to avoid this second step. I would think that the default model generated my SMILES input inside coot should at-least not have rings forming knots with each other. Also does anyone know if there is a way to flatten SMILES representations -i.e render them devoid of stereochemistry and then have libcheck do the most stable thing. I will crosspost later to ccp4bb in case this is a libcheck problem. Thanks in advance Hari
