[chimera-dev] adjust contour to mass

[Martin Turk]

Hi,

added another step for fine tunning and reduced number of steps, now it 
works much faster. Maybe there is a better way of doing the threshold 
steps. I overshoot up, down then up again, but it works :)

Best,
Martin



On 23.11.2013 16:29, Martin Turk wrote:
> Hi Shawn, Tom, Eric,
>
> thanks a lot for the help and for pointing me in the right direction. 
> Finally I had some time and I've come up with a script that adjusts 
> the volume level threshold from the active model to all opened models. 
> For one model it's not a problem, but when one wants to adjust the 
> levels for a series of volumes (for example after a 3d classification 
> run in relion), it becomes cumbersome to do so for the ~50 models/run. 
> Maybe other EM users find it handy, that's why I'd like to share it.
> It took me quite some time to find the right functions, which do the 
> actual measurement. Got lost in the OpenModels.h, volume.py, 
> volumedialog.py, and the gui scripts. The rest was easy :-) Thanks 
> again for your help!
>
> Best,
> Martin Turk
>
> Beckmann Lab
> LMU Gence Center Munich
>
>
> On 18.11.2013 20:49, Eric Pettersen wrote:
>> To supplement Shawn and Tom's answers, obviously it would be best if 
>> everything were documented, but in the absence of that if there is a 
>> command that implements something similar to what you want to do, you 
>> can chase it down in the code base by:
>>
>> a) looking at Midas/__init__.py and see if it's one of the functions 
>> in there (they're arranged approximately alphabetically by command 
>> name), and if it's not in there…
>> b) grep share/*/ChimeraExtension.py for the command name to find 
>> which module defines the command.  Then look in that module's 
>> ChimeraExtension.py to see what file/method in the module implements 
>> the command.
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>> On Nov 18, 2013, at 9:06 AM, Shawn Waldon <swaldon at cs.unc.edu 
>> <mailto:swaldon at cs.unc.edu>> wrote:
>>
>>> Hi Martin,
>>>
>>> I am not aware that there is a python library reference.  If there 
>>> is, I would appreciate a pointer to it as well.  Here are a few 
>>> links I have found helpful when writing python code for Chimera:
>>>
>>> This shows how to execute command line commands, it may be what you 
>>> want:
>>> http://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/ProgrammersGuide/basicPrimer.html 
>>>
>>>
>>> This goes through how to make plugins and such, but is helpful since 
>>> the examples show more of the API:
>>> http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html
>>>
>>> HTH,
>>> Shawn Waldon
>>>
>>>
>>> On Mon, Nov 18, 2013 at 9:10 AM, Martin Turk 
>>> <turk at lmb.uni-muenchen.de <mailto:turk at lmb.uni-muenchen.de>> wrote:
>>>
>>>     Hi,
>>>
>>>     I am trying to write a simple python script that will iterate
>>>     over opened volumes and adjust the contour level to a certain
>>>     mass. This shouldn't be more than ~10 lines. However, I can't
>>>     find chimera's python library reference to look up the class
>>>     structure and operator names.
>>>
>>>     Does someone know how, for example, set volume level to 0.01
>>>     would look like in python?
>>>     in the command line it would be for all models: volume #0-99
>>>     level 0.01
>>>
>>>     for models I've found chimera.openModels and then you can list
>>>     over them, but that's about it.
>>>
>>>     Thanks,
>>>     Martin Turk
>>>     _______________________________________________
>>>     Chimera-dev mailing list
>>>     Chimera-dev at cgl.ucsf.edu <mailto:Chimera-dev at cgl.ucsf.edu>
>>>     http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>>>
>>>
>>>
>>>
>>> -- 
>>> Shawn Waldon
>>> Graduate Research Assistant
>>> Department of Computer Science
>>> University of North Carolina at Chapel Hill
>>> swaldon at cs.unc.edu <mailto:swaldon at cs.unc.edu>
>>> _______________________________________________
>>> Chimera-dev mailing list
>>> Chimera-dev at cgl.ucsf.edu <mailto:Chimera-dev at cgl.ucsf.edu>
>>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>>
>

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