Dear Pascal, my suggestion to convince yourself that your ligand is there ..... 1. omit the atoms corresponding to your ligand from your pdb 2. compute electron density difference maps using data between 15-2.5A. High res maps (1.3-2.5A) will look worst than medium res maps if your ligand is partially occupied/mobile (typically bound on the surface of your proteins as opposed to a cavity). 3. Also, make sure you aren't wiping off the ligand by using an improper solvent masks during solvent flattening. If your ligand is really there, but not quite there.... you may try to pressure freeze your crystals instead of using conventional cryo-protectants. Good luck. Gino