Going back to the initial question. I would recommend looking at AFITT http://www.eyesopen.com/afitt
Works like a dream (in certain cases). Jürgen P.S. I wish I had some stocks from them but I don't ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Mar 12, 2013, at 11:25 AM, <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> wrote: You are the one who should judge your statement, but it looks plausible to me. Now that I think of it: why do we need referees if every scientist should judge their own hypothesis? Publication will be a lot faster if we no longer need to heed the remarks of some grumpy referees and send in revision after revision. Also the number of publications will increase significantly if every scientist is allowed to judge their own papers! HS ________________________________ From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu] Sent: Tuesday, March 12, 2013 4:14 PM To: Schreuder, Herman R&D/DE Cc: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk> Subject: Re: [ccp4bb] validating ligand density Dear Jacob, You are overinterpreting, the statement is about judging, not proving a hypothesis. I am sure Mr. Edwards judged his statement to be ok. I guess there is a good likelihood that you are right, but who am I to judge? JPK Herman ________________________________ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Jacob Keller Sent: Tuesday, March 12, 2013 3:44 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] validating ligand density 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<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Robbie Joosten Sent: Tuesday, March 12, 2013 10:03 AM To: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of > R.Srinivasan > Sent: Monday, March 11, 2013 23:03 > To: CCP4BB@JISCMAIL.AC.UK<mailto: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<mailto:kell...@janelia.hhmi.org> ******************************************* -- ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org> *******************************************
