[Chimera-users] Atoms outside volume

Tom Goddard goddard at cgl.ucsf.edu
Tue Mar 10 14:07:23 PDT 2009

Hi Tsutomu,

  I guess you want the atoms outside a given contour level of the 
volume.  There is a Chimera keyboard shortcut "oa" (outside atoms) to 
select those atoms.  If you don't use shortcuts (Tools / General 
Controls / Keyboard Shortcuts) you can run them as ordinary Chimera 
commands using the "ac" command:

    volume #0 level 2.5
    select #1
    ac oa

These 3 commands set the contour level for map #0, select all the atoms 
in PDB model #1, then run keyboard shortcut oa which changes the 
selection to just those outside the contour.  If you have multiple maps 
open, the "oa" shortcut is using the highlighted one in the volume 
dialog.  You can write the selected atoms to a file if desired with menu 
entry Actions / Write List....  If you really want atoms outside the 
volume bounding box, then just use a threshold less than the smallest 
data value (range shown in volume dialog).


Tsutomu Matsui wrote:
> Dear Tom,
> My name is Tsutomu Matsui, a postdoc in Jack Johnson Lab at Scripps 
> Resaerch Institute. I love Chimera very much.  I would like to select 
> all atoms inside or outside a volume file (density map). Is it possible?
> Thank you very much,
> Tsutomu

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