Hi again,
So the problem has been solved by adding a bond line into the CIF that
explicitely tells phenix that the "bond" should be 4 angstroms instead of
2.1. But I don't understand why Phenix would somehow see that these atoms
should be bonded together. This is a phenyl immidazole ligand with two
nitrogens, one of which is about 1.9 angstroms from the iron (a real
coordination). The other is about 4 angstroms. Why does phenix seem to want
to assign a bond between the nitrogen further away?
-Yarrow
On Monday, June 23, 2014, Yarrow Madrona
Hello,
I have a ligand bound to a heme and I have supplied a CIF for phenix in refinement. I did not include all atoms just, those close to the iron. Unfortunately, I am getting very large reported bond deviations for other atoms. For example I get:
bond pdb="FE HEM A 410 " pdb=" N3 CPZ A 500 " ideal model delta sigma weight residual 2.100 4.054 -1.954 2.00e-01 2.50e+01 9.54e+01
N3 and FE are not bonded and not expected to be close to one another. it is not supported by the structure. I suspect that this is causing my overall bonds deviations to be ~0.03 even if I greatly reduce the weight of wxc.
Is it necessary to enter all of these outliers into the .cif file or is there an easier way? Thank you.