Dear Anusman -
It actually looks like the refinement didn't go so badly (the atoms are
all in electron density), it's just that the Al - F bond lengths are a
bit too long for Coot to draw them as bonds.
I don't know what the correct bond distances should be (consult the
literature and the PDB for that), but if your refinement is not giving
you those bond distances, perhaps your molecule and the dictionary
restraints don't match. You should look at the section near the
beginning of the Refmac log file where it mentions disulfide bonds and
other non-standard bonds to be used. You're looking for the bonding
statements referring to the atoms of your ligand, like this:
$TEXT:Warning: $$ Potential and actual links $$
WARNING : link:NAG-ASN is found dist = 1.440 ideal_dist= 1.439
ch:AA res: 350 ASN at:ND2 .->Ab res: 601 NAG
at:C1 .
If the statement for your AlF3 says "link is found (not be used)" that
means your link restraints won't be applied in the refinement. The
usual result of this is for the atoms to drift apart from each other
somewhat; this would give you the result you see.
I hope this helps!
- Matt
On 1/16/15 2:07 PM, ansuman biswas wrote:
Dear users,
I have a data at 2.2 A resolution. I am able to model AlF3 into the
electron density (fig attached). However after one cycle of refinement
the AlF3 molecule is exploding and the atoms move apart (fig2).
AlF3 is already present in refmac library. First, I used that. But it
broke up after refinement.
Then, I extracted AlF3 coordinate from already published PDB and
prepared the cif file. But, it also failed. I modified the cif file by
changing the bond lengths according to the broken AlF3 structure but
it was of no help.
Kindly suggest how to carry out the refinement.
regards,
Ansuman
--
Matthew Franklin, Ph. D.
Senior Scientist
New York Structural Biology Center
89 Convent Avenue, New York, NY 10027
(212) 939-0660 ext. 9374
