Trajectory superposition question
Dear Madam/Sir, I have a long MD trajectory (dcd files), and before performing analysis on it I would like to superimpose every frame to the protein from the first frame or the protein from the average one. I am not sure how can this easily be performed. Thank you for your answer, Samo Lešnik
Dear Samo, If it is just to have a steadier view during playback with MD Movie, see “hold steady” option in MD Movie “Actions” menu. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html> However, normally this kind of processing is done with some other software (not Chimera) before you load the trajectory into Chimera for viewing. I don’t do this myself, but web-searching suggests it could be done with VMD plugin RMSDTT, or ptraj or cpptraj (in Ambertools). It is a common step of trajectory processing, so there are probably other programs that do it too. A good place to look may be in the documentation of whichever program was used to create the trajectory in the first place. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 12, 2018, at 4:53 AM, Samo Lešnik <samo.lesnik@gmail.com> wrote:
Dear Madam/Sir,
I have a long MD trajectory (dcd files), and before performing analysis on it I would like to superimpose every frame to the protein from the first frame or the protein from the average one.
I am not sure how can this easily be performed.
Thank you for your answer,
Samo Lešnik
Dear Elaine, thank you for your reply. I will then just use VMD plugins for this. I though more elegant to do the whole procedure in Chimera, however if not yet possible it is no problem. Best regards, Samo On Wed, Dec 12, 2018 at 8:15 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Samo, If it is just to have a steadier view during playback with MD Movie, see “hold steady” option in MD Movie “Actions” menu. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.h...
However, normally this kind of processing is done with some other software (not Chimera) before you load the trajectory into Chimera for viewing.
I don’t do this myself, but web-searching suggests it could be done with VMD plugin RMSDTT, or ptraj or cpptraj (in Ambertools). It is a common step of trajectory processing, so there are probably other programs that do it too. A good place to look may be in the documentation of whichever program was used to create the trajectory in the first place.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 12, 2018, at 4:53 AM, Samo Lešnik <samo.lesnik@gmail.com> wrote:
Dear Madam/Sir,
I have a long MD trajectory (dcd files), and before performing analysis on it I would like to superimpose every frame to the protein from the first frame or the protein from the average one.
I am not sure how can this easily be performed.
Thank you for your answer,
Samo Lešnik
participants (2)
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Elaine Meng -
Samo Lešnik