[phenixbb] phenix.refine and ligands

Nigel Moriarty nwmoriarty at lbl.gov
Mon Dec 19 08:18:48 PST 2011


Andrzej

Send me (off-line) the model PDB file and CIF file from eLBOW.

Nigel

On Mon, Dec 19, 2011 at 3:56 AM, AFL <alnyds at gmail.com> wrote:
> Hi,
>
>  I'm facing an extremely annoying 'problem' when refining structures with
> ligands.
>
>  When I try to refine a structure with a ligand inserted in coot from what I
> believe is refmac dictionary I'm getting following error:
>  Number of atoms with unknown nonbonded energy type symbols: 13
>    "HETATM 3279  OG2 FLC B   1 .*.     O  "
>    "HETATM 3280  CGC FLC B   1 .*.     C  "
>    "HETATM 3281  OG1 FLC B   1 .*.     O  "
>    "HETATM 3282  CG  FLC B   1 .*.     C  "
>    "HETATM 3283  CB  FLC B   1 .*.     C  "
>    "HETATM 3284  OHB FLC B   1 .*.     O  "
>    "HETATM 3285  CBC FLC B   1 .*.     C  "
>    "HETATM 3286  OB2 FLC B   1 .*.     O  "
>    "HETATM 3287  OB1 FLC B   1 .*.     O  "
>    "HETATM 3288  CA  FLC B   1 .*.     C  "
>    ... (remaining 3 not shown)
>
>  When FLC (citrate anion) is exported via libcheck and cif file is generated
> with phenix.elbow everything works fine.
>
>  Why is the phenix.refine not compatible with the refmac dictionary
> definitions?
>  Or maybe I am doing something wrong?
>
> Cheers, Andrzej
>
> --
>  alnyds at gmail.com               e-mail
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-- 
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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