[Chimera-users] Move atoms (selections) in Chimera

Eric Dawson eric.dawson at vanderbilt.edu
Mon Nov 14 10:17:39 PST 2005

On Mon, 14 Nov 2005, Thomas Goddard wrote:

> Hi Dan,
>   The only model building capabilities current in Chimera are commands
> addaa and swapaa which add and swap amino acids, and bond rotation
> capabilities.  We think creating capabilities for building models into
> density maps like the program O is too big a project.  Building models
> without reference to maps may be easier but I suspect molecular
> dynamics capabilities or at least energy minimization are needed to
> make that useful.  Chimera does not do MD calculations or energy
> minimization and again that is a big project we have been reluctant to
> take on so far.
>   If you think specific new model building capabilities would be helpful
> given the above limitations, explain them and we will be happy to consider
> them.
> 	Tom
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You guys might get away with just a 'quick & dirty' energy evaluation that 
includes a 'soft' steric repulsive term. This could be implemented in a 
manner similar to the 'scuplting' feature in Pymol.

Just a suggestion. This type of feature would be quite useful to our users 
at Vanderbilt in the Medical Center. Thanks for your consideration.


Eric S. Dawson, Ph.D.
CSB Computation, Education & Outreach
Research Instructor, Biochemistry
Center for Structural Biology (CSB)
Vanderbilt University

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