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Hi Zhen, You don't say what wavelength data you are refining against. But if you are near the edge, the dispersive effects will be large (close to -10 electrons at the Se inflection point). This changes the scattering factor. If you don't adjust the scattering factors to correct for f'. You will end up with some negative density on your Se atoms. Regards, Mitch -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Tuesday, September 26, 2006 11:08 AM To: [EMAIL PROTECTED] Subject: [ccp4bb]: Negative density arround Selenium *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Deal all, I recently solved a structure at 1.7A by MAD. However, there is always strong negative density arround all 8 selenium in the protein during CNS refinement. The Selenium-methionines fit 2fo-fc density well. I tried to use peak, edge or remote dataset with or without scale anomalous flag on and all did not matter. Does anybody have a solution for this matter? Thanks. Zhen
