Re: [phenixbb] Refinement

26 May 2015

      Dear mohamed noor,

in X-ray refinement one electron this way or the other would not make much
difference until you are working with data in the charge density region (below,
say 0.6A).
At normal resolution ranges you cannot distinguish really between N, C, O, so
for Fe with three times as many electrons, +2 or +3 wouldn't have much effect.

Best,
Tim

On Sat, May 23, 2015 at 07:01:01AM +0100, mohamed noor 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 
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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-- 
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149

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