Young-Jin

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 thus loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z 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 -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709     Email : [email protected] Fax   : 510-486-5909       Web  : CCI.LBL.gov