[phenixbb] CIF for Thiol-substituted DNA

Nigel Moriarty nwmoriarty at lbl.gov
Wed Aug 6 08:50:23 PDT 2014


Most of your problems arise because the PDB input format is subpar. It is
always better to use the three-letter code thus:

phenix.elbow --chemical-component=c2s

to get the attached.

In more recent versions of Phenix, nonstandard nucleotides produced by
eLBOW are automatically linked by phenix.refine although sometimes you may
need to specify link_all=True in some corner cases.

If you have any more trouble send me the model file.



On Wed, Aug 6, 2014 at 8:30 AM, Mark A. White <mawhite at utmb.edu> wrote:

>  Hello,
> I have a diThiol substituted phosphate on a CYT residue (C2S: S1P & S2P in
> place of O1P & O2P).  So far I have tried using phenix.elbow to produce a
> CIF, but with limited success.  First, the links to the neighbouring
> nucleotides are not created.  I could just add a links.cif to the input,
> but this would not include the DNA angle restraints. Second, the sugar-base
> chirality is not preserved, although it is listed in the CIF file.
> Is there a better way to produce a substituted DNA, similar to the example
> of adding the O5T to 5pho GUA?
> Also, why is the sugar-base chirality not preserved if it is in the CIF?
> C2S chir_03  C1'     O4'      N1     C2'    positiv
> the comand:
>     phenix.elbow --do-all dt15_C.pdb
> produced:
>     elbow.C2S.dt15_C_pdb.001.cif
> Thanks,
> Mark
>   --
> Yours sincerely,
> Mark A. White, Ph.D.
> Associate Professor of Biochemistry and Molecular Biology,
> Manager, Sealy Center for Structural Biology and Molecular Biophysics
> Macromolecular X-ray Laboratory,
> Basic Science Building, Room 6.660 C
> University of Texas Medical Branch
> Galveston, TX 77555-0647
> Tel. (409) 747-4747
> Cell. (281) 734-3614
> Fax. (409) 747-1404
> mailto://mawhite@utmb.edu
> http://xray.utmb.edu
> QQ: "All opinions are not equal. Some are a very great deal more robust,
> sophisticated and well supported in logic and argument than others."
> - Douglas Noel Adams (2002)
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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