What is the cell difference? Space group difference- surely not??? Between the two data sets. At lowish resolution the maps can tolerate more cel difference of course than at high resolution.. Eleanor
On Wed, 21 Nov 2018 at 13:09, Almudena Ponce Salvatierra < [email protected]> wrote: > Dear Pavel, > > thanks for the quick reply. Indeed, when I place the ligand where I > suspect it could be, the program says: The polder map is likely to show the > ligand. Indeed I see a blob ... > > I watched the video tutorial some time ago. It's very easy to use, indeed. > > Concerning the Fobs-Fobs maps, the program says: Crystal symmetry > mismatch. Calculations will continue using the symmetry in the pdb file, > but the maps should be treated with extreme suspicion. Here instead I don't > see any blob around "my preferred" location for the ligand > > I will check the paper more carefully > > Thank you very much > > All the best > > Almu > > El mié., 21 nov. 2018 a las 13:18, Pavel Afonine (<[email protected]>) > escribió: > >> Hi Almudena, >> >> I wonder to which extent I can trust the positive blobs or polder maps >>> that I am generating... >>> >> >> the answer to this question is given in corresponding paper that >> describes Polder map: >> http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf >> >> Based on the analysis described in this paper the program states the >> verdict in plain English (as opposed to a bunch of numbers). >> >> For a lazy option you can watch the video tutorial >> >> https://www.youtube.com/watch?v=TcTuMJayh5c&feature=youtu.be >> >> For even lazier option you can fast-forward to minute 4 of the video >> where Dorothee shows what to watch for. >> >> >>> Anybody that can make other suggestions concerning how to validate the >>> ligand binding site and/or generate other maps that could be more helpful? >>> >> >> If you have another data set collected from the crystal without the >> ligand and crystals are reasonably isomorphous, you can calculate Fobs-Fobs >> map. >> >> Good luck, >> Pavel >> > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
