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<p>Try adding the line:</p>
<p>wait</p>
<p>... before those two commands. That will tell ChimeraX to draw a frame and do all the associated processing before moving on.</p>
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<p id="reply-intro">On 2020-05-07 13:52, Caroline Stone wrote:</p>
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<p><span style="font-family: Calibri;">Dear All, <br /></span></p>
<p><span style="font-family: Calibri;">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.<br /></span></p>
<p><span style="font-family: Calibri;">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. <br /></span></p>
<p><span style="font-family: Calibri;"> </span></p>
<p><span style="font-family: Calibri;"> # ChimeraX script to imitate dynein 2 tail Toropova et al 2017 figure style<br /> # Adds custom colours to the ChimeraX session<br /><br /> # Open model and set camera view and model rotation<br /> open 6RLB <br /> windowsize 775 775<br /> 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<br /><br /> # Work with model representation<br /> surface #1<br /> set bgColor white<br /> lighting soft<br /> graphics silhouettes true<br /><br /> # Define custom colours<br /> color name midblue #6b80b5<br /> color name midgreen #a0c497<br /> color name midyellow #f9ef87<br /> color name midtomato #f97054<br /> color name midmagenta #a4449b<br /><br /> # Recolour model using custom colours defined above<br /> select #1/A; color sel midblue<br /> select #1/B; color sel skyblue<br /> select #1/C; color sel midtomato<br /> select #1/D; color sel midmagenta<br /> select #1/E/F; color sel midgreen<br /> select #1/G/H; color sel lightpink<br /> select #1/I-N; color sel midyellow<br /> select clear<br /><br /> # Open map and modify color and transparency<br /> open emdb:4918<br /> volume #2 step 1<br /> volume #2 level 0.0172<br /> surface dust #2 size 10<br /> color zone #2 near #1 distance 15<br /> volume #2 transparency 0.75</span></p>
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<p><span style="font-family: Calibri;">Best wishes, <br />Caroline<br /></span></p>
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