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<p><font face="Calibri">Dear All, <br>
</font></p>
<p><font face="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>
</font></p>
<p><font face="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>
</font></p>
<p><font face="Calibri"><br>
</font></p>
<p><font face="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</font></p>
<p><font face="Calibri"><br>
</font></p>
<p><font face="Calibri">Best wishes, <br>
Caroline<br>
</font></p>
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