pafonine at lbl.gov
Tue Apr 7 19:37:58 PDT 2015
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.
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
> 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
> HETATM 2 CL1 LIG 1 -0.441 6.507 20.373 1.00 0.00
> HETATM 3 CL2 LIG 1 3.190 7.731 21.231 1.00 0.00
> Thank you for Help.
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