[Chimera-users] Structure minimization for model with rigid body

danashah at post.tau.ac.il danashah at post.tau.ac.il
Mon Jan 14 23:13:18 PST 2013


Hi Elaine,

Thank you for the quick answer.
Good day,
Dana.

__
Dana Sachyani
Joel Hirsch's Lab
Faculty of Life Sciences
Tel Aviv University
Ramat Aviv, Israel
e-mail: danashah at post.tau.ac.il
Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Dana,
> Unfortunately there is no way to minimize and treat some part as a  
> (moving) rigid body.  You can only specify that some atoms should  
> not move at all, with the"spec" and/or "freeze" options.  The frozen  
> atoms will still exert forces on the others unless you also use the  
> "fragment" option to ignore them completely.
>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Jan 13, 2013, at 11:51 PM, danashah at post.tau.ac.il wrote:
>
>>
>> Hi all,
>> We're interesting in performing a structure minimization for a  
>> model, while treating a part of the model as a rigid body.
>> Is "fragment true" the best way to do that, or is there a different option?
>>
>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html#fragment
>>
>> Of course the "spec" option will define all the atoms which are not  
>> in the rigid body part....
>> Best,
>> Dana.





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