[phenixbb] Refinement

Nigel Moriarty nwmoriarty at lbl.gov
Sat May 23 08:47:30 PDT 2015


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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>
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