[phenixbb] How to tighten ligand geometry in phenix.refine?

Pavel Afonine pafonine at lbl.gov
Thu Aug 28 07:23:21 PDT 2014

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.


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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