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Dear all We are refining the atomic model of an icosahedral capsid based on a cryoEM map obtained from samples of intact viruses. The nominal pixel size of the map is 1.21 A and the resolution (according to Relion) is 3.9 A. We have tried to finely calibrate the map pixel size by running several refinements of the atomic model at different map magnification levels (phenix.auto_sharpen + phenix.real_space_refine with 2ry structure restraints and no ADP refinement). Results are quite confusing (see attached graphs, the nominal pixel size is represented by the black thick vertical line): * the best map-to-model fit is found at a rather larger pixel size (~1.35A) than the nominal one (1.21 A); * however the resulting icosahedral assembly is quite loose around 1.35 A pixel size (according to PISA predictions the 60-meric would not be stable); * also, quite a few Ramachandran conformations initially in favoured regions shift towards less favoured (though allowed) regions as the map-to-model fit increases. Do you have any suggestion on how to interpret these results or a better procedure (if any) to better evaluate the map magnification ? Cordially -- Stefano Trapani Maître de Conférences http://www.cbs.cnrs.fr/index.php/fr/personnel?PERS=Stefano%20Trapani ------------------------------------- Centre de Biochimie Structurale (CBS) 29 rue de Navacelles 34090 MONTPELLIER Cedex, France Tel : +33 (0)4 67 41 77 29 Fax : +33 (0)4 67 41 79 13 ------------------------------------- Université de Montpellier CNRS UMR 5048 INSERM UMR 1054 ------------------------------------- -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1