It would help if we knew the crystallization conditions and the protein solution components. Also, what are the map sigmas and e/A^3? It seems odd that there isnt positive density on the Fo-Fc map across the entire blob seen on the 2Fo-Fc map, considering you do not have anything modeled in. My guess is that your Fo-Fc map is at a much lower e/A^3 compared to your 2Fo-Fc map and what you are seeing is basically just greatly amplified noise. Try placing 3 waters in the blobs you see on the 2Fo-Fc map and see if that helps.
------------------------------------------------------------------------------- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -------------------------------------------------------------------------------- ** Hard work often pays of in time, but Procrastination always pays off now ** ----- Original Message ----- From: "stacy William" <stacy.biot...@gmail.com> To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, January 19, 2012 1:44:30 AM Subject: [ccp4bb] extra density ?? Dear All, I am working on plant proteins and solved a structure, there is an extra density which i cannot fix . I am attaching the coot image , can anybody suggest me what it could be THANKS :)
