[Chimera-users] Split map from command line

[armoelle]

Dear Tom,
Many thanks for your swift reply - 
Last night I found the problem with my script:

Originally, I first opened several maps and then split them - while color zone does work the ac sm command does not.
However, when I work in sequence - so opening, colorzone and then split it works without a problem. 
I guess this is related to you saying that the volume has to be active in the volume viewer and it might not be after I have opened another map.

Anyways…

Thanks again

cheers
Arne

> On 29. Oct 2018, at 18:29, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Arne,
> 
>  The keyboard shortcut “sm” for splitting a map based on the color zone coloring operates on the active volume — that is the one highlighted in Volume Viewer (it’s title above the histogram has a blue background).  If you are just opening maps then I think the most recent one is the active volume.  Ideally there would be a command and not just a shortcut to do this splitting operation.  I’ll add this to our new program ChimeraX.  You could use Python to do the splitting of say all maps by putting the following code in splitmap.py and using “open /path/to/script/splitmap.py”
> 
> from VolumeViewer import volume_list
> from ColorZone import split_volume_by_color_zone
> for v in volume_list():
> 	split_volume_by_color_zone(v)
> 
>  Tom
> 
> 
> 
>> On Oct 29, 2018, at 2:21 AM, armoelle <arne.moeller at biophys.mpg.de> wrote:
>> 
>> Dear Chimera Team,
>> 
>> I am trying to call the split map command directly from a script but somehow I don’t seem to be able to get it to run - maybe you can help me?
>> 
>> I am calling scolorzone (which works perfectly) and then ( as suggested in the mailing list) use the accelerator command ac sm to split the map. 
>> However, generally nothing happens - sometimes though (I don’t know what triggers it - and I am not doing anything different) it runs perfectly fine.
>> I am a bit puzzled as the same is the case no matter if I run form command line or I use the keyboard shortcuts gui. 
>> 
>> Many thanks for your help!
>> 
>> cheers
>> Arne
>> 
>> 
>> 
>> 
>> 
>> 
>> ________________________________
>> 
>> Dr. Arne Moeller
>> Independent Research Group Leader
>> Department of Structural Biology
>> Max-Planck-Institute of Biophysics
>> 
>> Affiliated Researcher 
>> DANDRITE, Aarhus University, DK
>> 
>> www.moeller-lab.com
>> www.biophys.mpg.de/en/moeller.html
>> 
>> Arne.Moeller at biophys.mpg.de
>> 0049 69 63033057
>> Max-von-Laue-Strasse 3
>> D-60438 Frankfurt am Main
>> Office L.1.015
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
>