[phenixbb] Geometry problems

Yarrow Madrona amadrona at uci.edu
Mon Jun 23 18:03:36 PDT 2014

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?


On Monday, June 23, 2014, Yarrow Madrona <amadrona at uci.edu> wrote:

> 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.
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