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 (<pafon...@gmail.com>) 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
