[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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