[phenixbb] elbow-readyset

Morten Grøftehauge mortengroftehauge.work at gmail.com
Mon Apr 13 13:45:35 PDT 2015


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 <pafonine at lbl.gov> 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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