[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

the comand:
    phenix.elbow --do-all dt15_C.pdb


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 

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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