hmm - crystallographically difficult. The usual way is to make a dictionary file from the chemical information about the ligand. try to build something obeying the chemical restraints into the density - refine those coordinates and validate them. Eleanor
On 19 September 2014 22:06, ansuman biswas <[email protected]> wrote: > Dear All, > > I have collected a diffraction dataset from a crystal soaked in a solution > containing the ligand of interest. > After refining a few cycles, I can see some density in the active site > pocket, but not so clear to model the ligand unambiguously. > > Is any tool available to validate whether the ligand is actually there or > not ? > The Twilight server appears to be for PDB files that have already been > deposited. > > thanks and regards, > Ansuman Biswas, > dept. of Physics, > Indian Institute of science >
