[Chimera-users] Reset surface programatically from python

Tom Goddard goddard at sonic.net
Mon Dec 30 13:40:33 PST 2013


Hi Thomas,

  The best way to set the contour level and also to turn off capping box faces is by calling the set_parameters() method.

	mod.set_parameters(surface_levels = [-1], cap_faces = False)
	mod.show()

  Tom



On Dec 30, 2013, at 1:32 PM, Thomas Hrabe  wrote:

> Thank you Tom,
> 
> the script parameter was what I was looking for.
> My headless chimera now exports those webgl html files.
> 
> One more question: if I display negative density, how do I programmatically set 
> Surface & Mesh options > Cap high values at box faces?
> 
> Thanks,
> Thomas 
> 
> On Dec 30, 2013, at 12:48 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
>> 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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