Hi Raja,

this should work (the rightmost Zn is shifted one space left as required by PDB format):

ATOM 1 Zn Zn A 1 1.059 -1.211 -15.432 1.00 16.89 Zn

let me know if it doesn't.

Pavel.

On 5/26/09 1:52 PM, Raja Dey wrote:

Hi Pavel,
I enclosed the line below:

ATOM      1  Zn   Zn A   1       1.059  -1.211 -15.432  1.00 16.89      A    Z

I also tried with 

ATOM      1  Zn   Zn A   1       1.059  -1.211 -15.432  1.00 16.89      A    Zn

None worked.

Raja 
----- Original Message -----
From: Pavel Afonine <[email protected]>
Date: Tuesday, May 26, 2009 12:40 pm
Subject: Re: [phenixbb] creating cif for Zn
To: PHENIX user mailing list <[email protected]>

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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