Thanks Oleg. This was fixed by increasing the default excessive_bond_distance_limit. My restraint file looks like : refinement.geometry_restraints.edits { excessive_bond_distance_limit = 15 C8_C1=chain C and resid 8 and name C1' D10_C1=chain D and resid 10 and name C1' bond { action = *add atom_selection_1 = $C8_C1 atom_selection_2 = $D10_C1 distance_ideal = 9.1 sigma = 0.02 slack = 0.5 } } And now it works! Thank you Oleg! Bradley On Thu, Jul 17, 2014 at 8:05 PM, Nigel Moriarty wrote:

Bradley

Send me your example off-line so I can test it and maybe modify.

Nigel

On Thu, Jul 17, 2014 at 12:52 PM, Bradley Hintze wrote:

...

Hey PHENIX,

I am wondering if I can define a distant restraint longer that 3A in a custom restraint file? The conventional way of doing this is to provide :

refinement.geometry_restraints.edits { C8_C1=chain C and resid 8 and name C1' D10_C1=chain D and resid 10 and name C1' bond { action = *add atom_selection_1 = $C8_C1 atom_selection_2 = $D10_C1 distance_ideal = 9.1 sigma = 0.02 slack = 0.5 }

Obviously this is a distant and not bond restraint. 9.1 exceeds the allowed length of 3 for a bond. Is there a different type of restraint that allows longer distances?

Thanks! -- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry

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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

-- Bradley J. Hintze Duke University PhD Candidate Department of Biochemistry