Standardized 3DVA movies

Hi, I would like to align multiple 3DVA simple outputs (volume series/movies) to systematically visualize them in a standard manner (same angle and scale in chimera). I am not sure if this is currently possible other than fitmap & resample individual frames. Align 3D maps job does not seem to get the job done with 3DVA or display as inputs, including when using lower-level results (maybe I did not try the right combination).
I want to make movies at the same viewing angle for multiple datasets in a standardized way. I guess it could work to orient each one with the same commands since they are all aligned to the same symmetry axis, so that might be the right method.

Also, when I follow the movie-making commands in the tutorial, my movies come out at slightly different speeds. I want to visualize two different angles simultaneously, so I am relying on the speeds being identical so I can combine them in another program. I think my computer has some slowdown during the chimera session that translates to slightly different output speeds. Any way to ensure identical frame-to-frame speed in the final output?


I agree, having the 3D maps at least aligned would be very helpful, I am not sure how complicated it is though considering how 3DVA processing works.

The only time I used 3DVA, all maps in a given trajectory had a consistent orientation relative to each other, so I don’t know how to help you with your first question.

Regarding frame rate in movies, assuming you are using ChimeraX, here is an example from some of my own work:

# Generate a movie going through the volume series

# The 'graphics rate maxframerate 30' command causes the resulting movie to be at 30 frames per second
# instead of whatever the default is in ChimeraX (I think it's 60); I chose 30 fps
# because it is the default export frame rate in Openshot, the movie editing software I subsequently 
# used to assemble several movie files into a single movie

# To adjust the number of steps through the volume series per second, you need to
# play with the 'pauseframes 15' and 'wait 900' numbers:
# I had 59 volumes and wanted to go through them at 2 volumes per second
# so 'pauseframes 15' keeps each step in the volume series displayed for 15 movie frames (so 0.5 s at 30 fps)
# before changing to the next volume
# and 'wait 900' makes the entire movie 900 frames (so 30 s at 30 fps)

view #1
graphics rate maxframerate 30
#Forward direction movie
vseries play #1 jumpto 0
movie record
vseries play #1 normalize true pauseframes 15; wait 900
movie stop
movie encode forward.mp4 framerate 30
# Reverse direction movie
vseries play #1 jumpto 9
movie record
vseries play #1 normalize true direction backward pauseframes 15; wait 900
movie stop
movie encode backward.mp4 framerate 30

In ChimeraX, run the command help <cmd> to learn more about all these commands and options, if my comments are not enough.

I hope this helps.

Thanks @Guillaume for sharing this! I will give it a go in chimeraX. I think my main issue at this point is the different speed of movie outputs caused by slowdowns on the computer while running “movie record,” even for different components of the same 3DVA display job.