<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Daojiong,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>There is no command for “Join Models”, but the Python equivalent isn’t too difficult. Let’s assume you’ve selected the C and N atoms by whatever means (and only those atoms), then this Python code would be the “Join Models” equivalent:</div><div class=""><br class=""></div><div class="">from chimera.selection import currentAtoms</div><div class="">a1, a2 = currentAtoms()</div><div class="">if a1.element.name == “C”:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>c, n = a1, a2</div><div class="">else:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>c, n = a2, a1</div><div class=""><br class=""></div><div class="">length = 1.33</div><div class="">dihedral = 180.0</div><div class="">phi = -120</div><div class="">from BuildStructure import cnPeptideBond</div><div class="">cnPeptideBond(c, n, n, length, dihedral, phi=phi)</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>If you put the above Python code into a file whose name ends in .py, then you can run it simply by opening the file. So if you named the file peptide.py, then something like this:</div><div class=""><br class=""></div><div class="">sel something-that-selects-just-C-and-N</div><div class="">open peptide.py</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I have attached the Python file because my mail program changes simple quotation marks into fancy ones that aren’t correct in Python.</div><div class=""><br class=""></div><div class="">—Eric<br class=""><div class="">
<div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"><br class="Apple-interchange-newline"> </span>Eric Pettersen</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class=""></div></div></div></body></html>