On Tue, Jan 11, 2011 at 1:24 PM, Nigel Moriarty
2. I was trying to model BeF3-. When I tried to get restraint file from the ReadySet, it always makes BeF3 instead of BeF3-. Is there any way I can fix the charge of the molecule? Also, I would expect it should be in the library as a kind of common inorganic molecule to mimic the phosphorus group. If so, could you let me know how I can get and use it?
The molecule is in the Chemical Components database as BEF. phenix.refine does not use the charge in refinement so you can use the file you have. If you really want to at the charge, its added as one of the fields for the atoms.
This is not quite correct; the charges do not (yet) contribute to the geometry restraints, but phenix.refine will interpret the charges in the element column of the PDB file, and adjust the X-ray scattering of the charged atoms. However, this is usually applied to metal ions, and since the charge in BeF3- will be delocalized, I don't think it makes sense in this case. -Nat