[phenixbb] Geometry problems

Nigel Moriarty nwmoriarty at lbl.gov
Mon Jun 23 19:25:38 PDT 2014


The inputs are likely telling it to form the bond as it's not an automatic
thing. Please send all inputs to Pavel and I, off-line.



On Mon, Jun 23, 2014 at 6:03 PM, Yarrow Madrona <amadrona at uci.edu> wrote:

> 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 <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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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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