[phenixbb] Long Distant Restraints

Bradley Hintze bradley.hintze at duke.edu
Fri Jul 18 04:57:30 PDT 2014


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 <nwmoriarty at lbl.gov> 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 <bradley.hintze at duke.edu>
> 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
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>
> --
> Nigel W. Moriarty
> Building 64R0246B, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>



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