What I would do - not net ideal! 1) the ASP looks in the wrong place - shift it into green density and one OE is probably a water.. 2) MET notoriously hard to model - I suspect there often are multiple conformations.. And of course at some wave lengths the S contribution should be down weighted by f' - the default is to use the S scattering for CuKa wavelength..
3) I think you need to flip the GLY O and then refit the adjacent residues 4) SER is often in 2 conformations - I suspect that is the case here.. Eleanor On 26 April 2012 22:03, Antony Oliver <antony.oli...@sussex.ac.uk> wrote: > Alaksa, > > 1) What rmsd / sigma are you contouring your density at ? i.e. are you > down in the "noise" or are you at a reasonable value for your Fo-Fc map? > > 2) It looks like some of your side-chains appear to have more than one > conformation - it's fairly easy in Coot to position and model both. > > Tony. > > --- > Mobile Account > --- > > On 26 Apr 2012, at 21:55, "Alaksa" <xtal.cc...@gmail.com> wrote: > > > > > Dear all > > I am refining the crystal structure of a protein (Rfree and Rvalue are > <25 and <20 A respectively). However, I am getting the negative density at > some places in the side chain of residues. All side chains are properly > fitting into the blue density, however red density blobs are also present > at the same place along with blue density . At some other place this red > density is also present in the main chain along with blue density (see the > attached snaps). If I have mutate the residues to alanine then density > becomes blue, but when change into the original residue, after refmac5 > again it is showing red blob. Also if I rotate the chain to place it in > green density, but after running refmac it attain original position having > red blob. I am not using TLS. > > I am seeking some strategy so that the problem can be solved. Please > suggest me the possible reasons and remedy. Also i am naive in > crystallography. > > > > Thanks > > Alaksa > > > > > > <coot2.png> > > <coot1.png> > > <coot3.png> > > <coot4.png> >
