In the absence of expert reply, my naive suggestion is: just make a 3-letter code up using elbow.get_new_ligand_code command-line tool. I can see this as three steps:

- run elbow.get_new_ligand_code to get 3-letter code;
- edit ligand PDB file to replace LIG with the new code;
- run elbow with the new PDB file.

Note, PDB file is a poor file to specify chemistry, use SMILES strings if possible instead.

Pavel

On 4/6/15 10:06 AM, Tarek DawoD wrote:

Dear All

if i have pdb file for CdCl2, how could i generate cif file (to use later in phenix.refine) from that using readyset or elbow or any other tool.
i could not find 3 letter could for CdCl2.

COMPND    UNNAMED                                                               
AUTHOR    GENERATED BY OPEN BABEL 2.3.1                                         
HETATM    1 CD   LIG     1       0.994   8.428  20.546  1.00  0.00          Cd  
HETATM    2 CL1  LIG     1      -0.441   6.507  20.373  1.00  0.00          Cl  
HETATM    3 CL2  LIG     1       3.190   7.731  21.231  1.00  0.00          Cl  
END

Thank you for Help.
regards
TK_DawoD



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