Hi Srinivasan,
I always use edstats from the command line: 'edstats.pl HKLIN 101m_0cyc.mtz XYZIN 101m_0cyc.pdb'. I hadn't noticed it was well-hidden (or the limit case: not present) in CCP4i. I guess a feature request is in order. Cheers, Robbie Date: Wed, 13 Mar 2013 03:42:45 +0800 From: sreera...@yahoo.co.in Subject: Re: [ccp4bb] validating ligand density To: CCP4BB@JISCMAIL.AC.UK Thank you very much to all those who suggested a way out for our situation. We have so far refined the occupancies on phenix and the ligand shows an uniform occupancy of 0.8 post the refinement. The B-factors of the ligand are around 20 (atleast for the regions with a well defined electron density), which is slightly lower than the average B-factors of the whole structure which is 24. We have a few poorly defined regions in our electron density. This was the starting point of our problem and it remains to be a problem. @ Robbie ---> we would like to run EDSTAT on CCP4 but we dont find the program in both 6.3.0 and 6.3.1 versions. It would be kind to know if we are doing something wrong to not find it on the ensuite. @ Herman ----> We did add the cryo from the crystallisation condition as another strategy but that also doesnt look too convincing. There is just that enough more to the density to think its our substrate. The density also does not compare well with the apo structures. @ Eleanor----> We set the occupancies to zero and refined the structure but we did not get any conclusive answers from it. We have a continious density for the best part of the ligand; but as you mentioned a few carbon atoms which are wobbly are poorly defined. We will look carefully into the geometrical restraints as you suggested. Thank you all again for the suggestions!Srinivasan From: "Bosch, Juergen" <jubo...@jhsph.edu> To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, 12 March 2013 4:32 PM Subject: Re: [ccp4bb] [ccp4bb] validating ligand density Going back to the initial question.I would recommend looking at AFITThttp://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> <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 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] On Behalf Of Jacob Keller Sent: Tuesday, March 12, 2013 3:44 PM To: 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] 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 ******************************************* -- ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *******************************************
