Write me a ChimeraX script that loads a set of mrc files labeled volume001.mrc through volumeN.mrc , sets them all to be cornflowerblue with a reasonable common isosurface level, then rotates them all to a known orientation specified in the script, and then records a movie of: cycles through all the images, rotates it 90 degrees along an axis, cycles them again, then saves the video to movie.mp4 .
user
Sure, I'd be happy to help with that. Here's a ChimeraX script that does that. Please replace `"my/path/to/volume001.mrc"`, `"my/path/to/volumeN.mrc"`, `"my/path/to/movie.mrc"`, and `"known/orientation"` with your actual paths and coordinates, respectively.

```
load 1 "my/path/to/volume001.mrc"
setView">"cornflowerblue"<>0.5,0.8>  # set color to cornflowerblue
setISO 1.0  # set isosurface level to 1.0 (adjust as needed)
setAnim 1  # set animation to on
setAutoUpdateAnim 1  # set auto-update animation to on
setAnimRange 0,90  # set animation range from 0 to 90 degrees
save 1 "movie.mp4"  # record video at the end

# Repeat this block for each volume file
load 2 "my/path/to/volume002.mrc"
copy3 1 2
setView">"cornflowerblue"<>0.5,0.8>
setISO 1.0
setAnim 1
setAutoUpdateAnim 1
setAnimRange 0,90

...

load 100 "my/path/to/volumeN.mrc"
copy3 1 100
setView">"cornflowerblue"<>0.5,0.8>
setISO 1.0
setAnim 1
setAutoUpdateAnim 1
setAnimRange 0,90

# Repeat this block for each volume file
load 101 "my/path/to/volume001.mrc"
copy3 1 101
setView">"cornflowerblue"<>0.5,0.8>
setISO 1.0
setAnim 1
setAutoUpdateAnim 1
setAnimRange 0,90

...

setView "known/orientation/x" "known/orientation/y" "known/orientation/z" < "known/orientation/alpha" "known/orientation/beta" "known/orientation/gamma"  # Set orientation
updateAnim  # Update animation
run 100  # Run animation for 100 cycles
```

Note that this script assumes that all the `.mrc` files are in the same folder as the script and that "known/orientation" is a three-word set of coordinates in ChimeraX format, i.e., 'x y z alpha beta gamma'.
assistant
Write me a ChimeraX script that loads a set of mrc files labeled volume001.mrc through volumeN.mrc , sets them all to be cornflowerblue with a reasonable common isosurface level, then rotates them all to a known orientation specified in the script, and then records a movie of: cycles through all the images, rotates it 90 degrees along an axis, cycles them again, then saves the video to movie.mp4 .
user
To create a ChimeraX script that meets your requirements, follow the steps below:

1. First, make sure you have ChimeraX installed and the `ffmpeg` tool for video encoding.

2. Create a new text file using your favorite text editor, and paste the following script into the file.

```
# ChimeraX script for loading MRC files, setting the color and isosurface, rotating, and recording a movie

# Set reasonable isosurface level, you may need to adjust the value
# depending on your volume data
# This script assumes that N in volumeN.mrc is a number with leading zeros, e.g., volume001.mrc, volume010.mrc, etc.

# Specify the number of volumes you have (replace X with the number of volumes)
number_of_volumes = X

# Specify a known orientation in the script (Euler angles in degrees as [azimuth, elevation, roll])
known_orientation = [0, 0, 0]

# Specify output movie dimensions (width, height)
movie_dimensions = [800, 600]

# Set common isosurface level
common_isosurface_level = 1.0

# Set volume color
color_cornflowerblue = [0.392, 0.584, 0.929]

# Load the volumes and set their properties
for i in range(1, number_of_volumes + 1):
    volume_name = f"volume{str(i).zfill(3)}.mrc"
    run(f"open {volume_name}")
    run(f"volume #{i} level {common_isosurface_level} color {color_cornflowerblue}")

# Rotate all volumes to the known orientation
run("turn {0} {1} {2} deg all".format(known_orientation[0], known_orientation[1], known_orientation[2]))

# Set up movie recording
run("movie record")
run("movie size {0} {1}".format(movie_dimensions[0], movie_dimensions[1]))
run("movie encode output movie.mp4")

# Animate the volumes by rotating and cycling through them
for rotation in range(0, 360, 90):
    for i in range(1, number_of_volumes + 1):
        run("modeldisplay #{i}")
        run("wait 1")
        run("turn y {0} deg".format(rotation))
        run("wait 1")
        run("modeldisplay #{i} off")
        run("wait 1")

run("movie encode input stop")

# Save the movie
run("movie write")
```

3. Replace the "X" in the script with the total number of `volumeN.mrc` files that you have and adjust other variables like output movie dimensions, known orientation, isosurface level, etc., as needed.

4. Save the file with a `.cxs` extension, e.g., `mrc_animation.cxs`.

5. Run the script in ChimeraX by either launching ChimeraX and opening the script with `File > Open` or executing the following command in your terminal:

```
chimerax --script mrc_animation.cxs
```
assistant