[phenixbb] restrains for nucleaic acid base pairs

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Tue Apr 7 10:30:54 PDT 2009

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...


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