Re: [Chimera-users] Recording movie from multiple dcd files

For this thread, and anyone else out there who is interested. My student Kyle Diller just published a javascript plug-in for watching and movie making multi-frame PDB files in ChimeraX (note this is not Chimera 1.13) https://cxtoolshed.rbvi.ucsf.edu/apps/moleculardynamicsviewer The main advantage is that it allows use of the VR headset to watch dynamics (via VR on and VR off at command line) For VR, you need to have steamOS with steamVR activated too. With or without VR, it also takes advantage of the new advanced shading available in ChimeraX. Dr Greg A. Babbitt Life Sciences Rochester Institute of Technology ________________________________________ From: Chimera-users on behalf of MARIA CLARA BLANES MIRA Sent: Wednesday, May 22, 2019 4:13 PM To: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recording movie from multiple dcd files Thank you very much Elaine. I will try your suggestions. Regarding the problem I am having because my computer hang when I loaded the three dcd files…, thank you Eric for your comments. I cannot resize the dialog window because it hangs just when I click on MD/Ensamble Analisis / MD Movie. Before having these problems, I obtained a window where I could browse and add the psf and dcd files but since I had the problem I obtain a white window saying Get Ensemble Info at the header. Nothing inside and I can’t resize it because the spinning wheel is there and I can’t do anything. I have reinstalled Chimera but I obtain the same white window and the spinning wheel when I try to start the MD Movie interface Thank you again for your help, clara

El 22 may 2019, a las 19:30, Elaine Meng escribió:

Hi Clara Blanes, If your computer hangs when you specify multiple DCD files in the dialog, I don’t think it will make any difference to use a metafile since the underlying process is the same.

Secondly, even if you successfully entered the multiple DCD files, there is no provision in the movie-recording dialog opened from the MD Movie tool to only show some fraction of the frames from each unless they are evenly spaced out (every Nth frame across the whole thing). I.e., you couldn’t just show the first 30 frames from each DCD. Although you can specify a range of frames to load, it is only one range per trajectory even if the trajectory includes multiple DCD files.

Instead, you could try just opening each DCD one at a time (with its PSF) file, then running a Chimera command script to

(a) start recording (command “movie record…”) http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html

(b) play the frames you want in your movie (command “coordset…”) http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html

(c) stop recording but do not create the movie file yet (“movie stop”)

...close that trajectory, open next one (PSF + DCD), run script to do (a)-(c) above, repeat until done. Or, if you need the structure from one trajectory to be matched in position to the previous trajectory, don’t close the first one until after you opened the second one and matched it onto the first.

Then put all the recorded images together into a single movie file (command “movie encode”). Actually, you can do all kinds of fancy other things before, between, and after playing the trajectories, such as rotating the structure (command “turn”), showing title text (“2dlabels”), adding extra frames where there is no motion (“wait”), etc.

See Making Movies, movie-related commands, and example movie command files such as “ball-and-socket motion” which includes playing a morph trajectory with “coordset”: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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On May 22, 2019, at 3:10 AM, MARIA CLARA BLANES MIRA wrote:

Dear Chimera users,

I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs.

I think I should use a metafile in this situation. Something like this:

namd(psf/dcd)

pam.psf

pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number?

Thank you in advance, Clara Blanes

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