[phenixbb] Refinement

[mohamed noor]

Hi Nigel

I was referring to the partial charge in the restraint file, which IMHO
should be translated to the model.

I have a second problem - I'm using the cif file for refinement but the
angles and bond lengths still get distorted. These are flagged as outliers
in phenix.refine. Why is it not using the values that I input? My
resolution is 3.8 A, but I still end up with positive density around all
the hemes. In fact, the problems with hemes are the cause of a large
majority of my outliers. I did a parallel refinement with and without the
restraint file - it doesn't make any difference.

Mohamed

On Sat, May 23, 2015 at 4:47 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:

> Mohamed
>
> I'm not sure what you mean.
>
> Firstly, I would hope you used the default restraints available in Phenix
> rather that generate restraints in eLBOW.
>
> Secondly, are you talking about the formal charge in the model file or the
> partial charges in the restraints file.
>
> Cheers
>
> Nigel
>
> ---
> 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
>
> On Fri, May 22, 2015 at 11:01 PM, mohamed noor <mohamed.noor34 at gmail.com>
> wrote:
>
>> Sorry to bring up an old thread. While tidying up my model before
>> deposition, I noticed that in eLBOW, the HEM restraint has a charge of 0
>> for the Fe atom. Shouldn't this be +2 or +3? Usually Fe atom gets reduced
>> by X-ray anyway. Or does this only matter for those doing molecular
>> dynamics?
>>
>> On Tue, Mar 31, 2015 at 10:21 PM, Edward A. Berry <BerryE at upstate.edu>
>> wrote:
>>
>>>
>>>
>>> On 03/31/2015 02:12 PM, Pavel Afonine wrote:
>>> ~~~~~~~~~~~~~~~~
>>>
>>>> In fact, the C atom is covalently linked to the nearest Cys, so the
>>>>> HEM side chain should be 'moved' into the density and the green blob
>>>>> shouldn't be there.
>>>>>
>>>>
>>>> Is this link defined anywhere in restraints used in refinement?
>>>>
>>>> Pavel
>>>>
>>>
>>> Here is an example of restraints for heme c.
>>> Values are from the high-resolution structure 1C75.
>>> Here residue 501 is the heme of course; and 37, 40, 41, and 160 are
>>> the C,C,H, and M in CxxCH---M heme c binding motif.
>>> I use HEC.cif for the heme parameters, but make sure the bond lengths
>>> in the vinyl groups are consistent with single bonds.
>>>
>>>   geometry_restraints.edits {
>>>      bond {
>>>       action = *add delete change
>>>       atom_selection_1 = chain D and resid 501 and name FE
>>>       atom_selection_2 = chain D and resid 41 and name NE2
>>>       symmetry_operation = None
>>>       distance_ideal = 1.99
>>>       sigma = 0.1
>>>       slack = None
>>>     }
>>>     bond {
>>>       action = *add delete change
>>>       atom_selection_1 = chain D and resid 501 and name FE
>>>       atom_selection_2 = chain D and resid 160 and name SD
>>>       symmetry_operation = None
>>>       distance_ideal = 2.33
>>>       sigma = 0.1
>>>       slack = None
>>>     }
>>>     bond {
>>>       action = *add delete change
>>>       atom_selection_1 = chain D and resname CYS and resid 37 and name SG
>>>       atom_selection_2 = chain D and resname HEC and resid 501 and name
>>> CAB
>>>       symmetry_operation = None
>>>       distance_ideal = 1.815
>>>       sigma = 0.1
>>>       slack = None
>>>     }
>>>     bond {
>>>       action = *add delete change
>>>       atom_selection_1 = chain D and resname CYS and resid 40 and name SG
>>>       atom_selection_2 = chain D and resname HEC and resid 501 and name
>>> CAC
>>>       symmetry_operation = None
>>>       distance_ideal = 1.815
>>>       sigma = 0.1
>>>       slack = None
>>>     }
>>>
>>>
>>>
>>>
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