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

[Tristan Croll]

Try adding the line: 

wait 

... before those two commands. That will tell ChimeraX to draw a frame
and do all the associated processing before moving on.

On 2020-05-07 13:52, Caroline Stone wrote:

> 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
> 
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20200507/4dbadc64/attachment-0001.html>