[phenixbb] CIF for Thiol-substituted DNA
Mark A. White
mawhite at utmb.edu
Wed Aug 6 08:30:46 PDT 2014
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
phenix.elbow --do-all dt15_C.pdb
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
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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