Dear Jeorge are the water molecules without electron density properly coordinated? These could be ghosts... Additionally, did you solve the structure by molecular replacement? If so, in your search model, do you see these water molecules at the same / nearby location? Again, those could be model bias. Finally, depending on your resolution, you can expect a certain amount of water molecule (depends on other factors, obviously). If you find 'too many' (difficult to define 'too many'), it might be one indication that you are over-refining things.
I know I did not answer your question, but hope this could help. Others will have better comments I guess. Cheers, Leo > On 19 Nov 2014, at 07:33, jeorgemarley thomas <kirtswab...@gmail.com> wrote: > > Dear All, > > I am sorry to ask this simple question, but I really need suggestions for > this. As the refinement has been done at 3.0 Angstrom after refinement the > water molecules were added by using "find waters" in coot. After adding water > refinement was done using Refmac 05. Now when I look on the added water > molecules some has density around it and some does not (even no red density > around it). Should I remove later water molecules. and again do the > refinement ? Please give some explanation also for this. as the R free and R > meas has reduced to some extent, also the r m s d contour of map level was > kept at 1.09 after refinement. I welcome your suggestions, thanks in advance. > > > Regards > > Jeorge >
