The real SG is most likely not P1. I asked Phaser to search for 4 molecules, it found 3. Thanks for the advice, I will try it out.
Best, Roger On Wed, Apr 26, 2017 at 2:50 AM, <herman.schreu...@sanofi.com> wrote: > 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 > -- 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
