[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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