[chimerax-users] Script to color zone a map according to the underlying model

[Caroline Stone]

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

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