Split map from command line
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@biophys.mpg.de 0049 69 63033057 Max-von-Laue-Strasse 3 D-60438 Frankfurt am Main Office L.1.015
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@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@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@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@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@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@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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armoelle -
Tom Goddard