[Chimera-users] Coordinates of atoms and volumes

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 20 10:42:14 PST 2017


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 at 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 at cent.uw.edu.pl>
> 
> 2017-11-16 19:17 GMT+01:00 Tom Goddard <goddard at 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 at 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 at cent.uw.edu.pl>




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