I don't get this. Are you doing small molecule crystallography with phenix.refine? Or are you using CdCl2 as a cover for a secret ligand? Because CdCl2 is highly water soluble. There shouldn't be a three-letter code for it. On Wed, Apr 8, 2015 at 4:39 AM Pavel Afonine wrote:

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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