Hi Nick, It sometimes helps tweaking the solvent mask settings. In Refmac the command for the option is 'solvent optimise'. PDB-REDO uses this function as well. Cheers, Robbie On 31 May 2019 10:53, Nicholas Keep <[log in to unmask]> wrote: There is no blue (2fo-fc) density at least at the current contour level in your difference density. That probably indicates what you are seeing is noise rather than a real feature. I am also seeing more intense (above 7 sigma in some cases) positive difference density without actual density in my current refmac refined structure than I am used to. I ascribed this to being in P1 with significant anisotropy leading to ripples???, but if this is widespread then there may have been tweaks to the software. Anyone else want to comment on this Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email [log in to unmask] Telephone 020-7631-6852 (Room G54a Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door ######################################################################## 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