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
    }

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org

_______________________________________________
phenixbb mailing list
phenixbb@phenix-online.org
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: phenixbb-leave@phenix-online.org