Hi Michał, To get map values at marker (= atom) positions and/or assign them as atom attributes, see command “measure mapValues” or the “Values at Atom Positions” tool. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#mapValues> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/density/density.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 20, 2017, at 2:18 AM, Michał Kadlof <m.kadlof@cent.uw.edu.pl> wrote:
Thank you, and how can I get the value of volume in the point where marker is?
-- pozdrawiam serdecznie Michał Kadlof <m.kadlof@cent.uw.edu.pl>
2017-11-16 19:17 GMT+01:00 Tom Goddard <goddard@sonic.net>: The Chimera getcrd command will report atom coordinates. In Python code you can get the coordinates for atom a with a.coord or a.xformCoord if you want to include the viewing direction.
To specify a point in a density map you usually put a marker on it with the Volume Tracer. A marker is actually and atom so getcrd works for that.
Tom
On Nov 16, 2017, at 3:36 AM, Michał Kadlof <m.kadlof@cent.uw.edu.pl> wrote:
Hi,
1. is there any way to get the exact Cartesian coordinates of any atom directly in Chimera?
2. Is there any way to get exact value from exact place inside density volumetric data?
-- best wishes Michał Kadlof <m.kadlof@cent.uw.edu.pl>