Mark

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.

Cheers

Nigel

On Wed, Aug 6, 2014 at 8:30 AM, Mark A. White <mawhite@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

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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,
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Nigel W. Moriarty
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