[phenixbb] Problem rebuilding ligand structure

[bsubedi at btk.fi]

Hi,

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:
HB3
“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,
Bishwa