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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