If you can narrow down the possibilities of compounds to a list of a few - let's say not more than 20...30 - then ARP/wARP 7 might be of help. It has a ligand building tool. One of its protocols is building an unidentified ligand from a list. Check the user-guide for detailed information on the usage.
Regards, Gerrit. > 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 â I do not know its atom > composition)? > > I hope someone could help. > > Thanks > > Ronaldo. > ------------------------------------------------- This mail sent through IMP: http://horde.org/imp/
