Hi,
Hard to say w/o moving the thing around, but it could be: pep flips, or even (less likely) wrong chain direction. Incidentally, some of thr the side chains 'just don't look right to me' - interpret that one as you wish but e.g. the leucine in the middle seems particularly wrong (try auto-find best conformer in Coot, I bet the opposite conformer is picked as the best).The very bottom-most residue's carbonyl doesn't seem to be in the density either. Suggestions: 1. Delete the top and bottom-most residues and execute real space refinement a few times - drag the carbonyls around manually and see what happens 2. Replace all residues with glycine, do the real space refinement, and then a few rounds of Refmac - see what comes up and rebuild sidechains. Artem "Nothing is built on stone; all is built on sand, but we must build as if the sand were stone" Jorge Luis Borges _____ From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Mike England Sent: Thursday, August 20, 2009 7:24 PM To: [email protected] Subject: [ccp4bb] electron density map Hi all, I will appreciate the comments on the 2Fo-Fc (1.5 sigma) and Fo-Fc (3.0 sigma) (at coot) maps as shown in attached picture . I am working at 3.0 A resolution (MR phasing with more than 80% homology) and current Rfree is 0.27 and FOM of 0.8. How to interpret the positive density (green) in Fo-Fc map which overlaps with the C-alpha tube? The side-chains of the polypeptide around this regions seems to be properly fitting and registry of the sequence seems to be OK. Is this due to some kind of model bias? Thanks in advance. Mike
