Hi Roger, First, sigma is a relative measure. If sigma is very low, e.g. since your map contains 80% solvent, 3 sigma may correspond to the same absolute value e.g. in electrons/Å3 as 1 sigma in a standard map, so I would not be worried about that.
However, an Rfree of 0.45 and a large off-origin Patterson peak indicates that you have to place another copy of your search molecule. This brings a few questions: - Is the real space group P1, or is there higher symmetry? In the latter case you have to move to the higher symmetry space group. - Did you ask phaser to search for 2 (or more) molecules? If the answer is no, that would be the first thing to do. - Otherwise, I would translate the molecule already found according to the off-origin Patterson vector and look how this fits into the electron density maps. Good luck! Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Roger Shek Gesendet: Mittwoch, 26. April 2017 03:23 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Contouring 2Fo-Fc map, large blobs in Fo-Fc Hi everyone, We have a structure that phaser found a solution for in P1, even though there is a large off-origin Patterson peak indicating pseudo NCS. However, the 2mFo-Fc map needs to be contoured up to >3 sigma to be reasonable, going lower makes it look like what I normally see at <1 sigma. If you look at the Fo-Fc map, there are large areas of positive and negative density. The 2mFo-Fc map looks very convincing, you can see the tyrosines, phenyl rings, etc...Also phaser gave LLG of >400 and a TFZ of ~14. Rfree is ~0.45. Does anyone know what's going on? Thanks, Roger -- Roger Shek Stony Brook University Graduate Student in Biochemistry and Structural Biology (PhD) Stony Brook Integrative Structural Biology Organization<https://sbintstrbio.wordpress.com/> Cell: (808) 386-3879
