[phenixbb] Problem rebuilding ligand structure

bsubedi at btk.fi bsubedi at btk.fi
Fri Jan 11 02:07:26 PST 2013


I am using Phenix 1.0-1069 for refinement and coot 0.7-pre-1 for visualization
and rebuilding. I used SMILES in coot to build the ligand and then merged them
with PDB.I had to do this as a separate step for both chains and the .cif file
so produced was not accepted for refinement.

I used readyset to obtain the restrains for refinement using .pdb file, even
though my refinement works, when i try to run real build refine in coot I get
this error message:

Failed to match (to the dictionary) the following model atom names:
“O6” “C10” “C11” “C12” “O7” “C13” “O5” “C8” “C9” ......
That would cause exploding atoms, so the refinement didn't start.

Could someone help me with fixing this problem.

Best regards,

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