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@scripps.edu -----------------------------------------------------------------