<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 10, 2011, at 8:53 AM, Elisabeth Ortega wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Chimera Dev. Team,<br><br><br>I have a little question for you. How can I select a bond using the Command Line (or the IDLE)?</blockquote><br></div><div>As Elaine mentioned, in the Command Line selecting atoms will also select the bonds between them. To select just one bond, you have to use Python/IDLE. This fragment of Python code would be used to get the bond between atoms a1 and a2:</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>b = a1.bondsMap[a2]</div><div><br></div><div>to cause it to become selected in the graphics window:</div><div><br></div><div>from chimera.selection import setCurrent</div><div>setCurrent(b)</div><div><br></div><div>[setCurrent make the selection the same as what you specify (i.e. the previous selection is replaced). You would instead use addCurrent if you want to add to the current selection]</div><div><br></div><div>Now, how you would get a1 and a2 is kind of up to you. If they were the only two atoms in the current selection, then this would do it:</div><div><br></div><div>from chimera.selection import currentAtoms</div><div>a1, a2 = currentAtoms()</div><div><br></div><div>I'd need to know more about your usage scenario in order to give any better advice. But maybe the above is good enough?</div><div><br></div><div>--Eric</div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br></body></html>