CIF for Thiol-substituted DNA
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)
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
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)
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participants (2)
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Mark A. White -
Nigel Moriarty