Hi Wulf,

first I would make sure that restraints applied to the cacodylate are correct. Do you specify these restraints yourself (provide ligand cif file) or let phenix.refine use whatever is available?

Data/restraints weight in phenix.refine is global. So if the weight was not optimal then everything else would have poor geometry, not only a particular molecule.

Pavel

On 8/28/14 7:08 AM, Blankenfeldt, Wulf wrote:

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

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