[Chimera-users] Reset surface programatically from python

Tom Goddard goddard at sonic.net
Mon Dec 30 12:48:38 PST 2013


Hi Thomas,

  I'm not sure why "chimera --send tmp.py" is not working.  But I am also confused why you are using the "--send" option?  That is intended to send the script to an already running Chimera (or starts a Chimera if it finds none running).  If that is not what you are aiming for you can just use "chimera tmp.py" or 'chimera --script "tmp.py 1.5 100"' if your script wants some arguments.  If you really are trying to send the script to an already running Chimera, report a bug using Chimera menu Help / Report a Bug… in Chimera (non-headless version) and explain that the problem is with the linux headless version.

	Tom


On Dec 30, 2013, at 12:40 PM, Thomas Hrabe  wrote:

> 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
>>> 
>>> 
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>> 
>> 
> 
> 




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