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Hello,<BR>
<BR>
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. <BR>
<BR>
Is there a better way to produce a substituted DNA, similar to the example of adding the O5T to 5pho GUA? <BR>
<BR>
Also, why is the sugar-base chirality not preserved if it is in the CIF?<BR>
<TT>C2S chir_03 C1' O4' N1 C2' positiv</TT><BR>
<BR>
the comand:<BR>
<TT> phenix.elbow --do-all dt15_C.pdb</TT><BR>
produced:<BR>
<TT> elbow.C2S.dt15_C_pdb.001.cif</TT><BR>
<BR>
<BR>
<BR>
Thanks,<BR>
Mark<BR>
<BR>
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-- <BR>
Yours sincerely, <BR>
<BR>
Mark A. White, Ph.D. <BR>
Associate Professor of Biochemistry and Molecular Biology, <BR>
Manager, Sealy Center for Structural Biology and Molecular Biophysics <BR>
Macromolecular X-ray Laboratory, <BR>
Basic Science Building, Room 6.660 C <BR>
University of Texas Medical Branch <BR>
Galveston, TX 77555-0647 <BR>
Tel. (409) 747-4747 <BR>
Cell. (281) 734-3614 <BR>
Fax. (409) 747-1404 <BR>
mailto://mawhite@utmb.edu <BR>
http://xray.utmb.edu <BR>
<BR>
QQ: "All opinions are not equal. Some are a very great deal more robust, sophisticated and well supported in logic and argument than others." <BR>
- Douglas Noel Adams (2002)
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