<div dir="ltr">Dale<div><br></div><div>You have done a lot of work on this and I'd really like the files that you have to date so I can make it easier in the future.</div><div><br></div><div>Regarding the hydrogens, I don't think Reduce will be able to help you. You may have to add them using Coot and then leave the hydrogens alone.</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>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" target="_blank">CCI.LBL.gov</a></div></div></div></div></div>
<br><div class="gmail_quote">On Thu, Dec 4, 2014 at 11:33 AM, Dale Kreitler <span dir="ltr"><<a href="mailto:dkreitler@chem.wisc.edu" target="_blank">dkreitler@chem.wisc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi All,<br><br></div>I am trying to add riding hydrogens to a model that includes beta-3-homoglutamine (B3Q). The monomer is not in the ccp4 library but it is a PDB chemical component. So far I have used elbow to build and optimize my own version of the ligand using the atom naming convention for a beta-amino acid in the PDB (where CB is in the backbone adjacent to the amino group, so the backbone goes like C-CA-CB-N). I am using a TRANS cif link from the monomer library for the N(alpha-amino acid) to C(beta-amino acid), and I have defined my own cif link for the N(beta-amino acid) to C(alpha-amino acid). However when I run phenix.reduce I can't get hydrogens to appear on the peptide bonds between the beta-amino acid and adjacent alpha-amino acids (hydrogens appear every where else on the ligand and in the model).<br><br>I realize the effect of two hydrogens on the model is inconsequential but I would like to figure out how I can get phenix.reduce to recognize the bonds to my "ligand" as standard peptide bonds and add hydrogens accordingly.<br clear="all"><div><div><br></div><div>Thanks,<br></div><div>Dale<span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888"><div><br>-- <br><div><div dir="ltr">Dale Kreitler<br></div><div dir="ltr"><div><div>Gellman Lab</div><div>UW Madison, Department of Chemistry</div></div></div></div>
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