Negative (or positive) density tells you what you that what you've
modelled is wrong.
If you have 1.15A X-ray data and it's telling you what you think is Ca2+
is not Ca2+, then I would think your X-ray data wins and your previous
structures lose (a lot can happen from one structure to the next...). I
must say, your 2fo-fc looks like a perfectly good Mg2+, since it is the
same size (ish) as the surrounding O and C atoms; a Ca2+ would have
given a much larger green blob.
phx.
On 30/06/2010 02:35, 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
