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 DROPBOX IMAGE: 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/
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... Pavel 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
DROPBOX IMAGE: 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/ _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (2)
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Jan Gebauer -
Pavel Afonine