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://[email protected] 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)