Hi Raja, normally phenix.refine should recognize Zn atoms without any problems and you don't need run elbow for this. If it doesn't, that most likely means your PDB file is ill-formatted (for example, no element type defined in 77(?) column). Could you please send me copy of the ATOM line from your PDB file containing Zn so I can tell what is wrong? Pavel. On 5/26/09 12:31 PM, Raja Dey wrote:
Dear Friends, I have Zn atoms in my pdb file. So, I think I need to run elbow to create the cif otherwise refinement stops. I did the following and got the error as follows:
phenix.elbow generate_easy_r4.pdb --do-all
------------------------------------------------------------------------------ electronic Ligand Builder & Optimisation Workbench (eLBOW) 1.4 3 - Nigel W. Moriarty ([email protected]) ------------------------------------------------------------------------------
Random number seed: 664322001 0:00 Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing Parsing P
No molecule read
Use --all-residues to view residues if this is a PDB file
Can anyone suggests at this point, what I should do? Thanking you in advance...
Raja
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