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

Nigel Moriarty nwmoriarty at lbl.gov
Tue Jan 11 13:24:17 PST 2011


> 1. First general question is regarding bond distance or van der Waals
> distance in the crystal structure. As I freeze the crystals as themselves ,
> I often see those distances are much shorter than what I normally expect in
> the refined structure. So how far they are acceptable or do we have any
> reference for bonds restraints in the crystal although ccp4 library should
> deal with these...

This first question is very complicated but there are small molecule
crystal structure that can be used for verification.

> 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. Just replace the periods with a value

BEF        BE      BE  BE    -1.         -0.1345   -0.0621   -0.3077
BEF         F1     F   F     0.         -0.3662   -1.1284    0.5141
BEF         F2     F   F     0.         -0.7111    1.0563    0.2239
BEF         F3     F   F     0.          1.2118    0.1342   -0.4303

Its currently not in the monomer library distributed with PHENIX but
you can easily generate a restraints file using

phenix.elbow --chemical-component=BEF


Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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