Dear all,

 

I am currently trying to refine a cacodylate ion that partially occupies the phosphate binding site of a PLP cofactor – partially meaning ~90%, in fact I am leaving the PLP out altogether.

 

When I am refining this in phenix. refine, the cacodylate becomes “ugly”: the tetraeder gets slightly squashed and the atoms are flying apart a bit such that they are not automatically connected in Coot any more. I am now wondering if I can tighten the geometry just for the cacodylate to prevent this from happening, either by sending a magical command or by fiddling with the dictionary. Can anyone advise me, please?

 

Regards,

 

 

Wulf