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

[Caroline Stone]

Hi Tom,

That is interesting, I see what you mean. I'll go ahead and update my 
installation. Thanks for the explaination!

Best wishes,
Caroline

On 07/05/2020 17:18, Tom Goddard wrote:
> Hi Caroline,
>
>   Tristan is right, although I think the command may need to be "wait 
> 1" which means draw one frame.  (The wait command without arguments 
> waits until ongoing motions complete and I'm not sure if it draws a 
> frame when there are no ongoing motions.)  The reason you need to draw 
> a frame is because the volume surface for your new threshold level is 
> not calculated until a frame is drawn.  In a script graphics are not 
> normally drawn until the end unless the wait command is used.
>
>   We saw this problem before and I put in a fix where volume surfaces 
> are recomputed when the level changes when running a script.  So your 
> script should work without any changes in the current ChimeraX daily 
> build.  That fix was made April 7, so I guess you are using a ChimeraX 
> older than that.  I'd suggest updating ChimeraX instead of adding 
> "wait 1" to your script.
>
> Tom
>
>
>> On May 7, 2020, at 6:02 AM, Tristan Croll <tic20 at cam.ac.uk 
>> <mailto:tic20 at cam.ac.uk>> wrote:
>>
>> 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
>>>
>>>
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