[Chimera-users] Smooth Trajectory in MD Movie Tool

[Yan Liang]

It works great. Thank you so much, Eric.

Sincerely,

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




On Apr 2, 2008, at 6:37 PM, Eric Pettersen wrote:

> 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).
>
> --Eric
>
> <avg.py>
>
> 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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