[phenixbb] How to treat EDTA on a special position

Pavel Afonine pafonine at lbl.gov
Tue Jun 25 11:24:02 PDT 2013

Hi Jan,

this is a perennial question that I keep addressing over and over (and 
keep forgetting what the good answer is). If you send me the files (off 
list, I need both model and data) then I will see what's the best way to 
handle this and then will add a corresponding section to phenix.refine 
manual. Normally it should just work but I might be forgetting something...


On 6/25/13 2:12 AM, Jan Gebauer wrote:
> Dear all,
> I recently solved a structure in R32/H (155).
> Interestingly some crystal contacts are mediated by an Metal/EDTA 
> complex.
> The metal -presumably a magnesium- sits on a special position (x,0, 1/2)
> in the middle of a twofold axis with the EDTA molecule coordinating it.
> (See "top" view in dropbox image below)
> If I fit the EDTA/Mg complex in the density, the symmetry will of course
> generate a symmetry mate on the same spot. (see "side" view in dropbox 
> image below). In
> phenix.refine, both entities are refined, which of course gives wrongs
> results.
> My question is, how to best define the Ligand to be compatible with
> phenix.refine and -later- with pdb submission.
> Should I just set occupancy to 0.5 for the whole EDTA molecule? - But 
> then
> I would still get two molecules at this site... Or split it somehow half
> and let the second half be generated by symmetry? In that case, I would
> need to define bonds over the asymmetric unit to prevent 
> "dissociation" of
> my ligand halves, wouldn't I? Or is there a third way?
> I already searched the phenixBB, but only found some "old" threads
> discussing vaguely similar problems. Unfortunately, they didn't help 
> me to
> answer which way is better... (or right...)
> Regards,
> Jan
> https://dl.dropboxusercontent.com/u/29745394/R32%20-%20EDTA.jpg
> -- 
> Dr. Jan Gebauer
> AG Prof. Baumann
> Institut für Biochemie / Uni-Köln
> Otto-Fischer-Str. 12-14 / 50674 Köln
> Fon: +49 (221) 470 3212
> Fax: +49 (221) 470 5066
> http://px.uni-koeln.de/
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