<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Okay, the executive summary for those interested is that in a case like this where minimization gets "stuck" on a large structure you may have to minimize badly distorted parts of the structure separately first by using the "fragment" option of the <i>minimize</i> command (<i>not</i> the "freeze" option in the tool or command, which still uses the remainder of the structure in the calculation).<div><br></div><div>--Eric</div><div><br><div><div>On Jan 2, 2013, at 1:34 PM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div 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>
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