<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Dec 29, 2012, at 7:40 AM, Damien Larivière wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Dear all,<br><br>I'm currently minimizing a circular DNA molecule, relatively large (~11 000 atoms). I use "Minimizing structure" in Structure editing.<br><br>The first phase, the Steepest Descent Steps, works fine.<br><br>However, the second one, the Conjugate Gradient Steps, looks like blocked with the message "dock prep finished" at the bottom of the screen.<br><br>If I remove one base pair so that the molecule is no more cyclized, then the second minimization stage starts as expected.<br><br>I'm not versed in the art of minimization. Do you know the reason of this behavior?</div></blockquote><br></div><div>Hi Damien,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I cannot reproduce this behavior. A small circular peptide (attached) minimizes fine with conjugate gradient. I need you to open a bug report (in Chimera, Help->Report A Bug) and attach the circular DNA structure. Thanks!</div><div><br></div><div>--Eric</div><br><div>
<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; "><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"></span>
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