[phenixbb] Another dictionary question...

Simon Kolstoe s.kolstoe at ucl.ac.uk
Fri Aug 8 09:43:46 PDT 2008

Thanks - Ralph solved my problem.

I looked in the cif dictionary and as I had originally added the NAG's  
using CNS the O1's were already removed. When I generated a dictionary  
using elbow, as the O1's were not present in the pdb coordinates, they  
did not get included in the dictionary - and hence the error. Not sure  
why it ran OK first time round...


On 8 Aug 2008, at 17:28, Ralf W. Grosse-Kunstleve wrote:

> Hi Simon,
>> RuntimeError: delete_atom_in_place: unknown atom_id: O1
> It is trying to delete the atom in the monomer library definition,
> as opposed to in the PDB file. It has to delete the atom in the
> monomer each time phenix.refine runs. So that looks OK.
> I'm guessing you somehow have the link twice. Could you look for
> a duplicate apply_cif_link block in your inputs? -- But I'm not
> sure that's it. If not, could you send me your inputs (directly,
> not to the list)?
> Ralf
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