Dear Pavel, 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? Thanks, Imre Pavel Afonine wrote:

Hi Imre,

you need to define custom bonds between these pairs:

http://phenix-online.org/documentation/refinement.htm

see section "Definition of custom bonds and angles".

phenix.refine does not do it automatically.

Pavel.

On 4/6/09 4:42 AM, Imre Toeroe wrote:

...

Hi,

Does anybody know an easy way to restrain nucleic acid base pairs (base stacking+Watson-Crick base pairing) in phenix.refine? I am refining against a 3.3 A dataset.

Thanks,

Imre

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb