[Chimera-users] Smooth Trajectory in MD Movie Tool

Eric Pettersen pett at cgl.ucsf.edu
Wed Apr 2 16:37:42 PDT 2008

Hi Yan,
	You _could_ write a script to do the averaging, but you would pretty  
much have to be an expert on how Chimera handles trajectory data to  
be able to write it in any reasonable amount of time.  Since I am  
such an expert, I've written the script for you and attached it to  
this message.  To do the averaging, simply have your trajectory open  
and then open the script (either with the File...Open menu or with  
the "open" command).
	Note that the script rewrites the coordinates of the trajectory.   
The only way to restore the trajectory to the "unaveraged" state is  
by reopening the original files.  The main parameter in the script  
you might want to change is the "window" variable, which controls how  
many adjacent frames contribute to the averaging.  The value in the  
script right now is 2, which means that the two frames to each side  
of a frame contribute to the average (with further-away frames  
contributing less).


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
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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