[chimera-dev] adjust contour to mass

[Martin Turk]

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
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>

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