[phenixbb] restrains for nucleaic acid base pairs

[Imre Toeroe]

Dear Ralf,

Thanks, that worked perfectly together with the coot given symmetry
operation.

Imre

Ralf W. Grosse-Kunstleve wrote:
> Hi Imre,
>
>   
>> Thanks for the info. One more question: In half of the DNA the base
>> pairing is between symmetry related bases as the DNA structure (Holliday
>> junction) lies on a two-fold axis. Could it be a problem?
>>     
>
> You need to define the symmetry_operation in this case, e.g.:
>
>   bond {
>     action = *add
>     atom_selection_1 = resname RXX and name NXX
>     atom_selection_2 = resname RYY and name NYY
>     symmetry_operation = -x,-y,z
>     distance_ideal = 2.8
>     sigma = 0.1
>     slack = 0.4
>   }
>
> A few days ago Marjolein Thunnissen told us about this trick for
> finding the symmetry_operation:
>
> : Luckily it is actually not that
> : difficult to find the symmetry operators when using coot. One just has to
> : switch drawing symmetry atoms on and clicking on a symmetry atom, coot will
> : tell you in the bottom line which atom it is and which symmetry operator was
> : used to draw it...
>
> Ralf
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