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

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 14 09:04:28 PST 2013

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.


I hope this helps,
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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