[Chimera-users] Circular DNA minimization

Eric Pettersen pett at cgl.ucsf.edu
Wed Jan 2 13:34:25 PST 2013

On Dec 29, 2012, at 7:40 AM, Damien Larivière wrote:

> Dear all,
> I'm currently minimizing a circular DNA molecule, relatively large (~11 000 atoms). I use "Minimizing structure" in Structure editing.
> The first phase, the Steepest Descent Steps, works fine.
> However, the second one, the Conjugate Gradient Steps, looks like blocked with the message "dock prep finished" at the bottom of the screen.
> If I remove one base pair so that the molecule is no more cyclized, then the second minimization stage starts as expected.
> I'm not versed in the art of minimization. Do you know the reason of this behavior?

Hi Damien,
	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!


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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