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@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@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Fri, May 22, 2015 at 11:01 PM, mohamed noor <mohamed.noor34@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@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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