[Chimera-users] Front End for NAMD?

Rudy J. Richardson rjrich at umich.edu
Mon Jan 7 17:20:29 PST 2013

Dear Eric,

You and the Chimera team are welcome to the kudos. I think it is amazing 
what Chimera does for free that major companies are charging for.

Regarding further development of Chimera as a GUI for NAMD, I really hope 
that someone might be persuaded to do this. As I said, I believe there is 
a real need for a new generation of MD interfaces that could open up the 
field. From what I have seen, I think it is possible that Chimera could 
provide an interface that is substantially better than anything currently 
available, and this would be a major contribution.

In any event, thanks for the existing elegance of Chimera and keep up the 
good work.

Best wishes,


On Mon, 7 Jan 2013, Eric Pettersen wrote:

> On Jan 6, 2013, at 7:47 AM, Rudy J. Richardson wrote:
>       To whom it may concern:
>       First, my profound thanks to the creators of Chimera for a
>       superb research and teaching tool. I am especially grateful for
>       the excellent interface with Modeller for doing such things as
>       creating and optimizing loops to repair chain breaks in X-ray
>       structures; this feature is greatly improved in v. 1.7rc.
> Dear Rudy,
> Thank you very much for the positive feedback.  We put in a lot of effort to
> make the 1.7 version of loop modeling more useful as well as easier to use,
> and to make it more bulletproof in the face of exotic input structures.
>  It's gratifying to hear that it's appreciated.
>       I am also grateful that Chimera can be used to visualize results
>       of MD simulations with, e.g., NAMD. However, in addition to
>       viewing results, it would be great if Chimera could be developed
>       to serve as an interactive GUI for setting up, running, and
>       analyzing NAMD simulations, including steered MD, as well. There
>       is a real need to make MD more accessible to a wider range of
>       scientists, and it appears that Chimera could be an excellent
>       platform for this. I realize that VMD has co-evolved with NAMD
>       for this purpose, but VMD lacks the integration, polish, and
>       intuitive ease of use of Chimera.
> Though we would love to provide this kind of interface, the reality is that
> we are a small team of programmers and therefore we really have to focus on
> additions and improvements that provide the most "value" to our user
> community -- which really largely translates into mostly providing unique
> features and capabilities not found in other packages, even if we might be
> able to provide them "better".  Also, it's quite difficult to propose to a
> funding agency that you are going to provide something that another package
> already provides, just a little bit better. :-)  So in practical terms this
> works out to the answer that Andrei already supplied -- you have to use the
> best available tool for the job.
> Nonetheless, there may be some related capabilities on the horizon.  Victor
> Munoz and J.D. Marechal are working on an interface to more of Chimera's
> MMTK capabilities.  Some initial fruit of this effort is the "Calculate
> Normal Modes" tool included in the daily build.  An interface to calculating
> MMTK MD runs is being worked on.  We are also thinking about including an
> interface to OpenMM for running MD trajectories.  That is still in a pretty
> preliminary phase.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
>                         http://www.cgl.ucsf.edu

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