Dear crystallographers, I hope someone could give me a hint to solve this problem. I have collected five datasets from the same protein and all of them, including the highest resolution data set (1.6 angstrons), display at the active site of the enzyme a very clear electron density with boundaries well defined. The problem is that I have already tried to fit all kinds of molecules present in the purification and crystallization conditions and none of them fit well into the density. Here are my questions: Is there any program available that could take a small volume of the electron density map (obviously the unidentified electron density ligand) and try to fit a list of known compounds (a list that I do not have, by the way) for potential ligands? Or, is there any website or program that could give me a list of compounds based only in the backbone of the ligand I could sketch from the density (by backbone I mean the plane shape of the compound – I do not know its atom composition)?
I hope someone could help. Thanks Ronaldo.
