On Apr 2, 2008, at 2:36 PM, Yan Liang wrote:
Thank you very much Eric. I have tried "Hold selection steady" function, and it helps a lot to reduce the overall movement of the large molecule. But as for the residuals, they are still very shaky.

I am thinking about writing a script to average the movement of each atom, but I have no experience in Chimera  scripting. Do you think it is possible to write such scripts in Chimera? Thanks.

Sincerely,

Yan Liang
Graduate Student
Department of Chemical Engineering and Materials Science
University of Minnesota



On Apr 2, 2008, at 1:42 PM, Eric Pettersen wrote:
Hi Yan,
Chimera doesn't yet support smoothing per se.  What you can do is use "Hold selection steady" in MD Movie's Actions menu to hold one or more atoms (possibly all atoms) as steady as possible across the trajectory -- which will mostly eliminate the translational component of the "shakiness".  This "holding steady" is most useful for small-molecule trajectories and replica-exchange trajectories.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Apr 2, 2008, at 10:44 AM, Yan Liang wrote:
Hi

I am using Chimera to make a MD movie. The problem is the movie is too  
shaky. Is it possible to smooth the trajectory by writing a Per-Frame  
script in MD Movie tool?

Thanks,

Yan Liang
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