[Chimera-users] Circular DNA minimization

[Eric Pettersen]

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 minimize command (not the "freeze" option in the tool or command, which still uses the remainder of the structure in the calculation).

--Eric

On Jan 2, 2013, at 1:34 PM, Eric Pettersen wrote:

> 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
> 
> <circular.pdb>
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