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Hi Gloria, My hobby is space group symmetry. My interest phenix development. > so I can't imagine a protein crystallographer > would ever need to apply the modulation function to a protein atom > that happened to be on one. That's true. Protein residues don't have internal symmetry, therefore they are not compatible with crystallographic special positions. (Wyckoff positions are enumerations of classes of special positions.) In the PDB molecules with internal symmetry are really rare, except for H2O and SO4. But these contribute so little to the total scattering that it isn't important to handle them in a special way. So Wyckoff positions remain foreign in the macromolecular context. Ralf ----- Original Message ---- > From: Gloria Borgstahl <[log in to unmask]> > To: [log in to unmask] > Sent: Wed, December 8, 2010 12:16:54 PM > Subject: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms > > I've gotten some interesting responses, that I will summarize for the > group later, but I thought I should clarify why I asked. > > I was worrying about this because I have been working out the steps in > how to determine the (3+1)D superspace group for a protein crystal. > The last step listed in IT vol C chapter 9.8, is to consider any atoms > that lie ON a Wyckoff position, and what restrictions this would apply > to the modulation function that is refined for each atom. > > My first reaction, was "Wyckoff positions?" I vaguely remember those, > my recollection from my experience was they were really cool, but were > usually in the solvent, so I can't imagine a protein crystallographer > would ever need to apply the modulation function to a protein atom > that happened to be on one. But to a crystallographer working on a > modulated mineral, it would happen all the time, I'll bet. > So maybe this was one more thing that just didn't really apply to > protein structures and lucky us > we don't worry about this last step (just as I never did model that > solvent water that was on one, back in the 90s). > > Then I thought, maybe I'm missing something, or there are special > cases out there (and so far I have heard of a disulfide bond on a > 2-fold connecting two homodimers). > > So I polled the collective knowledge of the great ccp4bb group. > > On Wed, Dec 8, 2010 at 10:57 AM, Gloria Borgstahl <[log in to unmask]> wrote: > > My fellow crystallographers, > > I wanted to take a poll. > > > > How many of you have ever had a protein atom on a Wyckoff position > > (AKA a special position). > > What kind of molecules have you found at special positions (it would > > have to contain the symmetry of the special position, right?) > > I'm thinking it is impossible to have a protein atom at a special position > > or am I exposing my ignorance yet again... > > > > my experience is that only once I found an atom in a special position, > > it was a strange solvent molecule, > > that blew my mind for a while until I learned about special positions > > in crystallography. > > > > Looking forward to your responses, Gloria > > > > ************************************************************************ > > Gloria Borgstahl > > Eppley Institute for Cancer Research and Allied Diseases > > 987696 Nebraska Medical Center > > 10732A Lied Transplant Center > > Omaha, NE 68198-7696 > > > > http://sbl.unmc.edu > > Office (402) 559-8578 > > FAX (402) 559-3739 > > > > Professor > > Hobbies: Protein Crystallography, Cancer, Biochemistry, > > DNA Metabolism, Modulated Crystals, Crystal Perfection > > Interests: Manga, Led Zepplin, Cold Play, piano, BRAN, > > RAGBRAI, golf and lately superspace groups > > ************************************************************************ > > >