Hi, you can't expect to see something with occupancy ~0.3 at the same cutoff level as you use to see fully occupied sites. So most likely the solution is to use a lower cutoff levels, as many suggested already. Two maps you attached look totally expectable to me.
Pavel On Fri, Jul 27, 2012 at 1:01 AM, Tri Ngo <[email protected]> wrote: > Dear ccp4bb, > > > I am working on refinement of an enzyme structure. I notice an alternative > conformation (gauche+ and gauche-) on both residues Phe and Tyr. > > > Here is the image of electron density before refinement. Based on the > different map intensity, I am quite sure there is an alternative > conformation on both positions. > > > http://i50.tinypic.com/29zaoap.jpg > > > However, after running occupancy refinement by Phenix, I don't see the > density map at the gauche- conformation of Tyr residue. Please take a look > at the image 2. > > > http://i50.tinypic.com/anzfrn.png > > > So do you think the gauche- conformation of Tyr exists in this structure. > Should I keep it in the final model because there is no positive map there? > > > > Thank you very much for your input. > > > -- > * > Ngo Duc Tri > > * > > PhD Student > Structural Biology Lab > > School of Medicine - Sungkyunkwan University - Korea > > Phone: 031-299-6150 - Cell: 010-7774-8210 > > >
