[Chimera-users] Circular DNA minimization

[Eric Pettersen]

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

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130102/77d0cb37/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: circular.pdb
Type: chemical/x-pdb
Size: 9487 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130102/77d0cb37/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130102/77d0cb37/attachment-0001.html>