Dear All,

As an exercise in scripting, I am trying to write a script to imitate the appearance a published figure (from Toropova et al 2017). I would like to display a semi-transparent map which has been color zoned to match the underlying model in surface view.

ChimeraX does everything in the script apart from the last two commands, in which I color zone the map, and then make it transparent. I don't get any errors in the log to give me a clue what to change. If I omit these last two commands from the script and then make them manually from the command line after the script is finished, it works. Is there something I can change that would allow me to include the final two commands in the script? Any pointers would be much appreciated.

    # ChimeraX script to imitate dynein 2 tail Toropova et al 2017 figure style
    # Adds custom colours to the ChimeraX session

    # Open model and set camera view and model rotation
    open 6RLB
    windowsize 775 775
    view matrix camera -0.30533,0.56038,0.76991,623.53,0.82837,-0.24247,0.50499,467.83,0.46967,0.79195,-0.39016,-7.3434 models #1,1,0,0,0,0,1,0,0,0,0,1,0

    # Work with model representation
    surface #1
    set bgColor white
    lighting soft
    graphics silhouettes true

    # Define custom colours
    color name midblue #6b80b5
    color name midgreen #a0c497
    color name midyellow #f9ef87
    color name midtomato #f97054
    color name midmagenta #a4449b

    # Recolour model using custom colours defined above
    select #1/A; color sel midblue
    select #1/B; color sel skyblue
    select #1/C; color sel midtomato
    select #1/D; color sel midmagenta
    select #1/E/F; color sel midgreen
    select #1/G/H; color sel lightpink
    select #1/I-N; color sel midyellow
    select clear

    # Open map and modify color and transparency
    open emdb:4918
    volume #2 step 1
    volume #2 level 0.0172
    surface dust #2 size 10
    color zone #2 near #1 distance 15
    volume #2 transparency 0.75

Best wishes,
Caroline