Export 3DVA results in chimera as movie

3D Variability Analysis
1

Hi, all!
I met a problem after doing the 3DVA.
I used the “simple” mode in the 3DVA. And I opened the 20 frames in Chimera via “volume series”. Now it can be a video in the Chimera. However, I wanted to export the video as .mp4 or other file type. How can I realize it? I am so sorry maybe it is a question about Chimera. But I believed that maybe someone here can give me a suggestion. Thanks a lot!

2

Chimera question, LOTS of useful resources on google and YouTube for chimera or chimeraX about Movie Maker. Quick tip if you’re on Mac, command + shift + 5 should record movie of any portion of the screen for any amount of time. Just play series and record

3

Hi @Yuqi I often use the following method with chimera.

Step1 : Volume Series setting

  • Play direction: oscillate
  • Check ‘Normalize threshold levels’
  • Check ‘Cache 30 renderings’
  • Data cache size : 1024 Mb

Step2 (optional) : Disable auto adjusting of step upon opening maps

  • Volume Viewer > Features > Data display options
  • Uncheck “Adjust step to show at most …”

Step3 (optional) : Always open maps with the default grey color

  • Volume Viewer > Features > Data display options
  • Uncheck “Initial colors”

Step4 (optional) : Set appropriate windows size

  • Specify width x height (in pixels) of movie with windowsize command.
  • For example: windowsize 480 480

Step5 : Create movie

  • Try this command. (Assuming the volume series is model #0)

vol all hide; movie record; vop morph #0 playStep 0.05 frames 20; wait 20; movie encode ~/test.mp4 framerate 20

To generate a movie of N round-trips of the volume series, replace the argument of ‘frames’ and ‘wait’ by 40 * N. For example to make a 2 round-trip movie,

vol all hide; movie record; vop morph #0 playStep 0.05 frames 80; wait 80; movie encode ~/test.mp4 framerate 20

(‘framerate’ should be left at 20)

Hope this helps

4 Likes
4

Hi @kttn,
Thanks so much for the detailed command line to make the movies. I got an issue when I was making my movies from 3DVA 20 mrc maps which are kind of big. vop morph #0 always gave me a bin=4 map in the movies. How to keep step=1 in Chimera during vop morph #0? I searched but failed to find the solution. Greatly appreciate your suggestions!

5

in the volume viewer tool above the threshold slider there is a step size indicator with drop down. you might need to readjust this for the volume created by the morph, which can also be independently adjusted for threshold btw. You can also change “Features” in volume viewer to show the “Data display options” and change the value for “adjust step” so it is never anything but step1 automatically and then save this as the default.

6

@CryoEM2 ,

Your suggestion worked! Thank you very much!