> > One final quote that is not in the twilight paper summarizes it nicely: > > "The scientist must be the judge of his own hypotheses, not the > statistician." > A.F.W. Edwards (1992) in Likelihood - An account of the statistical > concept > of likelihood and its application to scientific inference , p. 34. >
There must be a lot of thinking behind this statement--while it seems plausible, it seems far from proven prima facie. Also, it assumes that the scientist is not a statistician. Jacob > Btw, the book is good reading. > > Best, BR > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Robbie > Joosten > Sent: Tuesday, March 12, 2013 10:03 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] validating ligand density > > 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 > -- ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *******************************************
