Dear Srinivasan, Although the Twilight program can only look at deposited PDB entries, the tips about ligand validation in the paper are very useful. I suggest you start from there. You can use EDSTATS in CCP4 to get real-space validation scores. Also look at the difference map metrics it gives (and the maps themselves of course), they will tell you whether you misidentified your ligand. Occupancy refinement in Refmac can also help you: if the occupancy drops a lot something is wrong. That can be partial binding (not that much of a problem) or worse, a ligand that isn't there. By the way, I've been playing with that recently and some ligands/hetero compounds in the PDB were so incredibly 'not there' that Refmac would crash (that bug seems to be fixed in the latest version).
HTH, Robbie > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > R.Srinivasan > Sent: Monday, March 11, 2013 23:03 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] validating ligand density > > Hello all, > > We co-crystallized an inactive variant of our enzyme in the presence of > substrate and have determined the structure at 1.85A. > > Now, we want to validate the fitting of the ligand into the electron > density. We tried validating using the difference map (2Fo-Fc) after refining > the structure without the ligand. But, it is still a bit inconclusive if the density > fits the ligand. > > It would be very kind to know if there are tools for validating this > electron density. We were excited about twilight but turns out it can only be > used with deposited structure. > > > We will appreciate your help and suggestions. > > > Many thanks, > Srinivasan
