[Chimera-users] Atoms outside volume

Tsutomu Matsui tmatsui at scripps.edu
Tue Mar 10 14:25:46 PDT 2009

Hi Tom,

Thank you very very much. I made it! Tsutomu

Tom Goddard wrote:
> 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).
>    Tom
> 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

Tsutomu MATSUI, Ph.D.
Research Associate
The Scripps Research Institute
Department of Molecular Biology        Voice: +1-858-784-8280
10550 North Torrey Pines Road, MB-31   Fax:   +1-858-784-8660
La Jolla, CA  92037                    Email: tmatsui at scripps.edu

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