<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Hi Yasser,</div><div><br></div><div>On Jun 24, 2010, at 8:41 AM, Yasser Almeida Hernández wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi...<br>I want to connect two atoms that belongs to different models with a pseudobond. It's that possible with Chimera?</div></blockquote><div><br></div>Absolutely. That's the purpose of psuedobonds, to show non-covalent interactions between models such as hydrogen bonds, NMR constraints, hydrophobic interactions, etc.</div><div><br><blockquote type="cite"><div>If it does, how would be the Python API code?</div></blockquote><br></div><div>First I should mention that you don't necessarily need to use Python to do this. The PseudoBond Reader tool can create pseudobonds between models. But if you are writing a Python script anyway, you would first create a PseudoBondGroup to contain your pseudobonds like so:</div><div><br></div><div>from chimera.misc import getPseudoBondGroup</div><div>grp = getPseudoBondGroup("my pseudobonds")</div><div><br></div><div>and the create a pseudobond between atoms a1 and a2 with:</div><div><br></div><div>pb = grp.newPseudoBond(a1, a2)</div><div><br></div><div>--Eric</div><div><br></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>