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
