<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Apr 26, 2010, at 3:36 AM, Elisabeth Ortega wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear all,<br><br>I'm trying to place a fragment in certain position. I did this (on<br>Python IDLE):<br><br>from BuildStructure import placeFragment<br><br>placeFragment( fragment, resName, model = 'scratch', position=None)<br><br><br>Where fragment = benzene and resName = RING6 but I am not sure about<br>that . <br>Could you give me an example of placeFragment code?</div></blockquote><br></div><div>Hi Elisabeth,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>This will place a benzene ring at the center of the view in a new residue named "BZN" in a new model named "scatch":</div><div><br></div><div>from BuildStructure import placeFragment</div><div>from BuildStructure.Fragment import RING6, fragDict</div><div><br></div><div>placeFragment(fragDict[RING6]["benzene"], "BZN")</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Let me know if you have more questions. Though the placeFragment function does have some documentation, the Fragment.py file doesn't. Sorry about that.</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>P.S. I cc'ed the chimera-dev mailing list on this since that list deals more with programming questions.<div><br></div></body></html>