[phenixbb] pdb file error

Pavel Afonine pafonine at lbl.gov
Wed Dec 3 11:04:41 PST 2014

Hello Maher,

this means your PDB file contains a molecule that cannot be matched 
against known molecules in Phenix dictionary. Can you please send me PDB 
file and I will be able to tell more.


On 12/3/14 10:55 AM, maher alayyoubi wrote:
> Hi Everyone,
> I am having a problem of phenix.refine not accepting a pdb file that I 
> just finished editing in coot. It is a protein RNA compplex where the 
> protein part was built in buccaneer and the RNA strand built in 
> nautilus. I assembled the final model by text editing the pdb file and 
> adding the RNA part.
> Whenever I feed this pdb file into phenix, it comes back with two 
> errors: " number of atoms with unknown unbonded energy type symbols:6" 
> . "The coot command could not be located"
> Does anyone know how to fix this problem?
> I tried converting the file into mmcif and feeding it to phenix but 
> the same error comes back again.
> Thank you very much,
> Maher

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