<div dir="ltr">Mark<div><br></div><div>Most of your problems arise because the PDB input format is subpar. It is always better to use the three-letter code thus:</div><div><br></div><div>phenix.elbow --chemical-component=c2s</div>
<div><br></div><div>to get the attached.</div><div><br></div><div>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.</div>
<div><br></div><div>If you have any more trouble send me the model file.</div><div><br></div><div>Cheers</div><div><br></div><div>Nigel</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 6, 2014 at 8:30 AM, Mark A. White <span dir="ltr"><<a href="mailto:mawhite@utmb.edu" target="_blank">mawhite@utmb.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><u></u>
<div>
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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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. <a href="tel:%28409%29%20747-4747" value="+14097474747" target="_blank">(409) 747-4747</a> <br>
Cell. <a href="tel:%28281%29%20734-3614" value="+12817343614" target="_blank">(281) 734-3614</a> <br>
Fax. <a href="tel:%28409%29%20747-1404" value="+14097471404" target="_blank">(409) 747-1404</a> <br>
mailto://<a href="mailto:mawhite@utmb.edu" target="_blank">mawhite@utmb.edu</a> <br>
<a href="http://xray.utmb.edu" target="_blank">http://xray.utmb.edu</a> <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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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a>
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