On 28/01/15 21:05, ansuman biswas wrote:
Dear All,
I checked the Mg2+ B factor, and it was around 22. So, were the values
for F atoms. For AlF3, it was more than 50 for Al and more than 40 for
F atoms. I will take care about the occupancy. I hope that will fix
the small negative density.
When I inserted MgF in COOT using the code MGF (get monomer), it did
appear but looked fragmented. It remained fragmented after refinement
as well (as shown in the previously attached fig). But, there was no
warning about bond breaking in the Refmac log file. Even the density
of MgF3- looked better (2Fo-Fc).
If I see the structure in Chimera or CCP4MG, it does not look fragmented.
So, is it a problem of display in COOT?
Yes.
Is the exploded MgF3 form, not actually a broken form, since the
refinement log file does not show any such indication?
Yes. You have stumbled across an obscure idiosyncrasy of Coot's bonding
algorithm (it doesn't see bonds in residues where all the bonds are
longer than 1.71A). You might call this a bug. (Incidentally the
dictionary values for the bond length is 1.985A.)
Paul.
