[Chimera-users] crop a map via commandline

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 9 10:16:29 PDT 2017


Hi Edoardo,
The “region” option of the “volume” command is the same as setting region min and max in the Region bounds section of the GUI.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions>

For example, if I have a map #3, then command:

vol #3 region 10,10,10,20,20,20

is the same as GUI:

Region min max step  x[10 20 1 ] y [10 20 1 ] z [10 20 1 ]

That adjusts the display.  If you want to save this region to a file, you could instead use the “save” option,  for example, a command something like:

vol #3 save /Users/meng/Desktop/test.mrc saveRegion 10,10,10,20,20,20

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Oct 9, 2017, at 5:11 AM, Edoardo D'Imprima <eddimpri at biophys.mpg.de> wrote:
> 
> Dear Chimera users,
> is there an equivalent of Volume viewer/Features/Region bounds from the GUI to precisely crop several maps via command line? I tried a combination of volume region and vop zone subregion but it doesn’t really do what I would like to obtain.
> Many thanks in advance,
> Edoardo




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