[Chimera-users] Reset surface programatically from python

Thomas Hrabe thrabe at sanfordburnham.org
Mon Dec 30 13:32:57 PST 2013


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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