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

David E. Konerding dekonerding at lbl.gov
Mon Nov 21 11:28:02 PST 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.

No, it would be sufficient to have a "sprout atom by type" which would
only involve bond length, bond angle, and torsion terms,
all of which are already available.  The idealized geometry is already
available from the AMBER force field.

I've developed a C++ code which implements the AMBER force field (and
have been working on some Python wrappings, but it's a very low priority
project).  It doesn't do minimization or dynamics (I planned to use the
Gnu Scientific Library for that but it's also low priority).  I'd be
happy to make this code available under a reasonable (IE BSD) license so
that it could be included in Chimera.  It would be acceptably fast for
minimizing models
built using sprouting.


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