<div><br></div>Hi Glenn,<div><br></div><div>You can combine the segments in Chimera into one PDB. What I usually do is</div><div>go to Favorites->Model Panel (which lists all the segments open in your current</div><div>
session), then there is a button on the right labeled 'copy/combine'. You would</div><div>want the combine functionality.</div><div><br></div><div>Check the following for the Model Panel window:</div><div><meta http-equiv="content-type" content="text/html; charset=utf-8"><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html</a></div>
<div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html"></a>Alternatively, there's a command-line version of 'combine' (which I haven't used</div><div>yet); details here:</div>
<div><meta http-equiv="content-type" content="text/html; charset=utf-8"><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html</a></div>
<div><br></div><div>Just to add, I would recommend minimizing the structure after combining the</div><div>segments. This can be done in Chimera with Tools->Structure Editing->Minimize</div><div>Structure. Also, besides checking the distance between the C and N atoms,</div>
<div>you would want to make sure they are in the trans configuration for peptide bonds.</div><div>In my limited experience, the minimization doesn't always fix peptide bonds that</div><div>start in the cis configuration.</div>
<div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html"></a>Hope this helps,</div><div>Tim<br><br></div><div><br><div class="gmail_quote">On Tue, Jun 7, 2011 at 5:30 PM, Glenn Millhauser <span dir="ltr"><<a href="mailto:glennm@ucsc.edu">glennm@ucsc.edu</a>></span> wrote:</div>
<div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word">Hi Folks,<div>   I am trying to add a four amino acid segment to the N-terminus of a protein in the pdb.  I can generate the four residue stretch and move its C-term close to the N-term of the structured protein.  I can then select the C' and N atoms, which are about 1.0 Angstrom apart.  At that point, I am stuck.  Not sure how to add a bond and then create a proper structure.  I've played around with Join Models, but no luck.  Without a peptide bond recognized by Chimera, ribbons are discontinuous.  Any ideas?</div>
<div>Many thanks,</div><div>glenn<br><div>
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<br><br></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font>Glenn L. Millhauser</font></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font>Department of Chemistry & Biochemistry</font></div>
<div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font>UC Santa Cruz</font></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font>Santa Cruz, CA 95064</font></div>
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<br></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><a href="mailto:glennm@ucsc.edu" target="_blank">glennm@ucsc.edu</a></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px;min-height:14px">
<br></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px"><font><a href="http://chemistry.ucsc.edu/~glennm" target="_blank">http://chemistry.ucsc.edu/~glennm</a></font></div><div style="margin-top:0px;margin-right:0px;margin-bottom:0px;margin-left:0px">
<a href="http://www.chemistry.ucsc.edu/faculty/millhauser.html" target="_blank">http://www.chemistry.ucsc.edu/faculty/millhauser.html</a></div><div><br></div></span><font size="3"><span style="font-size:12px"><br></span></font></div>
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