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
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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