[phenixbb] 2 quesions: 1. bond and vdw restraints; 2. cif file for BeF3-

Nathaniel Echols nechols at lbl.gov
Tue Jan 11 13:33:22 PST 2011

On Tue, Jan 11, 2011 at 1:24 PM, Nigel Moriarty <nwmoriarty at lbl.gov> wrote:
>> 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.


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