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

[Elaine Meng]

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
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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.