[phenixbb] Long Distant Restraints

Nigel Moriarty nwmoriarty at lbl.gov
Thu Jul 17 17:05:14 PDT 2014


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
>
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> phenixbb at phenix-online.org
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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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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