[phenixbb] Problem rebuilding ligand structure

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jan 11 15:15:23 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.

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


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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> phenixbb at phenix-online.org
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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