Thanks James and all of you, The occupancy had to be lowered to 0.25 to get the B-factor similar to the coordinating atoms. But now I can see a good positive density. Ivan
On Tue, Jun 29, 2010 at 7:49 PM, James Holton <[email protected]> wrote: > > This kind of thing happens when the metal is not at 100% occupancy. Or if > it not what you think it is (Mg instead of Ca, for example). Depending on > your refinement program, you can do occupancy refinement or a "poor man's > occupancy refinement" where you adjust the occupancy manually and then > refine the B factors. When your unknown atom has a B factor similar to its > neighbors, you are probably at about the right occupancy. > > -James > > > On 6/29/2010 6:35 PM, xaravich ivan wrote: > >> Dear CCP4BB, >> >> I have come across something that might be pretty obvious to experienced >> people but is making me crazy. >> I have this great 1.15 angs data and I know that I have a Calcium ion >> (pics attached) from previous structures of the same protein, that I have >> solved. Rightly when I add waters with Arp solvent it does not put water at >> that positive density. >> Now whenever I have tried to put the calcium, and refine the structure it >> is giving me a negative density at the metal site. I csn see that the 2fc-fo >> is clear there, but why negative density. This is just the start of my >> refinement and I have to refine multiple ligands in the structure and I >> would like to get past this issue before that. >> >> I tried putting atom at the pointer, adding water and renaming it >> according to the naming convention in the PDB for Calcium, but nothing. >> >> Your suggestions would be invaluable, as always. >> >> Ivan >> >> >
