[Chimera-users] Reset surface programatically from python

Thomas Hrabe thrabe at sanfordburnham.org
Mon Dec 30 12:40:45 PST 2013


Thank you.

My script now works on my workstation.
On another linux machine where I am running the headless chimera, it is not processed.

I start it with

chimera —send tmp.py

but all I end up in is the chimera console.

Any suggestions?
Thanks,
Thomas

On Dec 30, 2013, at 12:05 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Thomas,
> 
> 	You need
> 
> mod.show()
> 
> to have the density map recompute its contour surface.   You can remove the mod.display = True line.  Your code 
> 
> mod.surface_levels = [-1,0]
> 
> is setting two contour levels one at density value -1 and one at 0.  Is that what you intend?  If you only wanted a single level you would use 
> 
> mod.surface_levels = [-1]
> 
>  Tom
> 
> 
> 
> 
> On Dec 27, 2013, at 3:24 PM, Thomas Hrabe  wrote:
> 
>> Hi everyone,
>> 
>> I have this line of code where I want to load a density and export a negative surface of it:
>> 
>> import chimera as ch
>> mod = ch.openModels.open(‘./density.em')[0]
>> mod.surface_levels = [-1,0]
>> mod.display = True
>> ch.exports.doExportCommand('WebGL', 'tmp.html’)
>> 
>> However, the surface of the density is rendered for positive values.
>> How can I refresh the display after I specify the surface_levels?
>> 
>> Thanks,
>> Thomas
>> 
>> 
>> _______________________________________________
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>> Chimera-users at cgl.ucsf.edu
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>> 
> 




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