[phenixbb] creating cif for Zn

[Pavel Afonine]

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 (NWMoriarty at LBL.Gov)
>  ------------------------------------------------------------------------------
>
>  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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