Re: [Chimera-users] Smooth Trajectory in MD Movie Tool
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  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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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Yan Liang