And here is an excellent Polder tutorial https://www.youtube.com/watch?v=TcTuMJayh5c
you can watch on YouTube in the Phenix Tutorials channel Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Thu, Feb 9, 2017 at 3:45 PM, Pavel Afonine <[email protected]> wrote: > > In addition to excellent Kay's reply.. > > Also make sure to check refined B factors. Note, if the ligand is not > there then that volume is likely filled with bulk-solvent. Now low > occupancy in combination with very large B factors may approximate > bulk-solvent quite well. The Polder map along with three CC values that its > calculation procedure reports should give you the answer whether the ligand > is there or not. > > Pavel > > > On Wed, Feb 8, 2017 at 2:43 AM, Kay Diederichs < > [email protected]> wrote: > >> Dear Petr, >> >> if I understand correcty, the mFo-DFc density (1) shows almost nothing, >> but the 2mFo-DFc (2) as well as the composite omit map (3) show the ligand? >> >> As you say, the apparent contradiction between (1) versus (2)&(3) is >> unexpected. One explanation could be that the Fc are simply too bad, i.e. >> the model not good enough to result in useful signal in the difference >> map. OTOH, that you see the ligand in (2) may be simply model bias, so is >> not meaningful. (3) is hopeful since there is no model bias. >> >> I would suggest to >> - refine the occupancy, to find out why the density is so weak >> - calculate a (Fo,soak - Fo,native) (4) map with phases from a model >> unbiased by the ligand >> - try a Polder map (5) >> >> - If the occupancy is around 0.5 or higher, that would be a good sign. >> - but if you don't see density in (4) and (5), then your ligand is >> probably not there in any useful amount >> >> I consider (4) as the most sensible method to show presence of the >> ligand, and it should convince reviewers. >> >> HTH, >> >> Kay >> >> >> >> On Wed, 8 Feb 2017 09:05:50 +0100, Petr Kolenko < >> [email protected]> wrote: >> >> >Dear colleagues, >> > >> >we have a dataset with potential enzyme:ligand complex at 2.2 AA >> >resolution. The ligand is very good substrate for the enzyme, we used >> >soaking. We do not see the ligand in the regular difference electron >> >density, only five out of twenty atoms. However, the ligand placed at >> >the active site (model used from structure of a mutant variant) is >> >refined well, giving no negative peaks in difference electron density >> >map and nice observed electron density. I have calculated composit omit >> >map with annealing in Phenix (input model did not contain the ligand) >> >and the electron density for the ligand is there. >> > >> >I have my own opinion, but we are desperate to obtain such data (more >> >than 40 crystals already tested). My question is, would this be proof of >> >presence of the ligand with reduced occupancy? Will this map convince >> >the reviewers? Is there any other way to validate presence of the ligand? >> > >> >Best regards, >> >Petr >> > >
