Hi Ivan,
these Dale Tronrud's slides might help you with understanding the maps:
http://www.ccp4.ac.uk/courses/stwk10/talk_files/Dale_The_Wonderful_World_of_Maps.pdf
Good luck!
Pavel.
On 6/29/10 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
>
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