[Chimera-users] Smooth Trajectory in MD Movie Tool
liangyan at cems.umn.edu
Wed Apr 2 19:17:19 PDT 2008
It works great. Thank you so much, Eric.
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).
> 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.
>> 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
>>> Eric Pettersen
>>> UCSF Computer Graphics Lab
>>> On Apr 2, 2008, at 10:44 AM, Yan Liang wrote:
>>>> 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-
>>>> script in MD Movie tool?
>>>> Yan Liang
>>>> Chimera-users mailing list
>>>> Chimera-users at cgl.ucsf.edu
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