On Fri, Jan 11, 2013 at 2:07 AM, wrote:

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.

Did you load the CIF from ready_set into Coot first? (File menu -> Import CIF dictionary) -Nat

Bishwa 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.

Why? Can you send me the files directly?

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:

It would be better to generate the restraints using the SMILES in eLBOW and then pass the restraints file to ReadySet!. Send me the file and we can fix them Nigel NB. Any files sent to me will be held in strictest confidence.

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

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