[phenixbb] Linking C-Type Heme

Edward A. Berry BerryE at upstate.edu
Tue May 23 15:03:45 PDT 2017



On 05/23/2017 03:55 PM, Julian Esselborn wrote:
> Hi list,
> that might sound like a stupid question, but we are having some trouble getting phenix.refine acknowledging a c-type linkage of a heme. That is a covalent Cys SG bond to C18 or C25 in the heme.
> The pdb file does contain a LINK record for this, but Ready Set seems to ignore that even if told to look for LINK records.
> The distance in the model is actually around 1.9 Ä and automatic ligand linking is on and set well below that distance.
> Any ideas why this might be failing and what is the smartest way to proceed?
>
> Any ideas highly appreciated.

If you are using the command line you can set it up with refinement.geometry_restraints.edits
Easiest in a .eff file. Here is what I use (residues 37 and 40 are the cysteines, 501 is the heme (HEC)).
I guess automatic linking kicks in if the atoms are _closer_ than the set threshold?

refinement {
. . . .
   geometry_restraints.edits {
     bond {
       action = *add delete change
       atom_selection_1 = chain 'D' and resid 37 and name SG
       atom_selection_2 = chain 'D' and resid 501 and name CAB
       symmetry_operation = None
       distance_ideal = 1.79
       sigma = 0.2
       slack = 0
     }
     bond {
       action = *add delete change
       atom_selection_1 = chain 'D' and resid 40 and name SG
       atom_selection_2 = chain 'D' and resid 501 and name CAC
       symmetry_operation = None
       distance_ideal = 1.79
       sigma = 0.2
       slack = 0
     }
. . . .
}










>
> Thanks a lot
>
>
>
> Julian Esselborn
>
> Tezcan Lab
> UC San Diego
>
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