That looks really odd - the whole MET has a negative/positive ghost
Second conformations usually branch at the CB, and dont look like that. Are you sure you havent somehow got two MET residues in the coordinate set ? Turn on cysmmetry display in coot and look for clashes around there. Does the rest of the map look OK? I would set the occupancies of the MET and nearby side chains to 0.00 (you can do that in coot) then refine and look at the maps again. This is very old fashioned but you can do this: distang xyzin coords.pdb dist inter end to get a list of close symmetry clashes & contacts Eleanor On 12 November 2014 09:17, Greg Costakes <gcost...@purdue.edu> wrote: > Hi Jeorge, > > The simplest answer is that you have multiple positions for the > Methionine. So you can try adding in an alternate position for it. However, > you didn’t mention the sigma cutoff or e-/A^3 for either of your density > maps. Its quite possible that your fofc map is just scaled way down and > what you are seeing is an exaggeration of what’s barely there. Hope this > helps. Cheers! > > - Greg > > > ------------------------------------------------------------------------------- > Greg Costakes, Ph.D. > Department of Biochemistry > University of Cambridge > 80 Tennis Court Road > Cambridge, CB2 1GA > United Kingdom > > -------------------------------------------------------------------------------- > > *From:* jeorgemarley thomas <kirtswab...@gmail.com> > *Sent:* Wednesday, November 12, 2014 8:16 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Refinement with refmac05 and methionine density > > Dear All, > > I am refining the structure with refmac05, and after each refinement the > density around this methionine is flipping. and it is difficult to say > where this methionine actually have the density. please suggest what I > should I do. I am attaching the snap here. > > Thanks in Advance for your kind suggestions > > Jeorge > > > > > ------------------------------ > <http://www.avast.com/> > > This email is free from viruses and malware because avast! Antivirus > <http://www.avast.com/> protection is active. > >
